Supplementary information for: Signals of recent positive ...

Supplementary information for: Signals of recent positive selection

in a worldwide sample of human populations

Joseph K. Pickrell1,†, Graham Coop1,12,†, John Novembre1,2,

Sridhar Kudaravalli1, Jun Li10, Devin Absher4, Balaji S. Srinivasan6,7,8,9,

Gregory S. Barsh3, Richard M. Myers4, Marcus W. Feldman5,

and Jonathan K. Pritchard1,11,†

1 Department of Human Genetics, The University of Chicago.2 Department of Ecology and Evolutionary Biology, UCLA.

3 Department of Genetics, Stanford University.4 HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL.

5 Department of Biological Sciences, Stanford University.6 Stanford Genome Technology Center, Stanford University7 Program in Biomedical Informatics, Stanford University

8 Dept. of Computer Science, Stanford University9 Dept. of Statistics, Stanford University

10 Dept. of Human Genetics, University of Michigan11 Howard Hughes Medical Institute.

12 Current Address: Department of Ecology and Evolution, University of California, Davis

† To whom correspondence should be addressed: [email protected],

[email protected], [email protected]

January 12, 2009

1

Power simulations. To estimate our power to detect selection in the ascertained Illuminadata, we performed simulations under the “cosi” model of human demography [3] with a slightmodification– for computational efficiency, the recent increases in population size were dropped.This had little effect on the fit of the model to the HapMap data (results not shown). Other rele-vant parameters are described in the main text. The selection model is one where a single selectedsite arises and sweeps up in frequency. Implicitly, this assumes a given selected locus in the humangenome has experienced only a single selective sweep in the time from over which our statisticsare applicable (approximately 10-80ky); we find this reasonable, and simulations of this kind are astandard method for testing the power of a test for selection [2, 4–7]

To approximate the ascertainment of the Illumina panel, we performed a two-stage ascertain-ment on all of the simulations; this is described in the main text. In Supplementary Figure 1, weshow that this procedure provides a good approximation to the frequency spectrum of the Illuminachip. For calculations of power, in all cases the selected site was excluded from analysis, makingthe calculations conservative. In Supplementary Figure 2, we show power estimates as a functionof derived allele frequency in different demographies, and in Supplementary Figure 3, we show theeffect of sample size on power.

About 200 of the simulations have a selected allele that arises on the branch common to boththe “European” and “Asian” populations; this allows us to get an upper bound on the expectedamount of overlap between the populations for XP-EHH (with a selection coefficient of 1% almostall selected alleles that arose during that branch would have gone to fixation and are not likely tobe detected by iHS). In these simulations of truly shared selective sweeps, 76% are detected in bothpopulations.

Overlap of haplotype-based selection signals between populations. We calculated iHSand XP-EHH in each individual population, and converted scores to empirical p-values as describedin the text. For a signal to be considered overlapping between populations, we required that theiHS or XP-EHH score be in the 1% tail of one population and the 5% tail of the other. InSupplementary Figures 4 and 5, we show the fraction of selection signals that overlap betweenall pairs of populations. The striking difference between African and non-African populations inXP-EHH is an artifact of the way XP-EHH is calculated–for non-African populations, we used thegroup of Bantu speakers as a reference, and for African populations we used a group of Europeanchromosomes as the reference. We performed the test this way to most closely follow what was mostpowerful in the simulations, but this means that the non-overlap between African and non-Africanpopulations by XP-EHH is not meaningful.

Calculation of the CLR statistic and overlap with other signals of selection The CLRtest used in the main text as an alternative to XP-EHH for detecting high-frequency sweeps wasoriginally designed to be applied to data for which SNP ascertainment is constant across the genomeand, ideally, can be properly modeled. This is not the case for the HGDP data–tag SNPs wereidentified in the HapMap database, which has complicated and often unknown ascertainment [1].

2

Because of this, we have used this statistic not as a formal test for significance, but rather to rankregions by the deviance of the allele frequency spectra from the genome-wide average. We then usedthe CLR statistics as test statistics like XP-EHH and iHS and convert them to empirical p-valuesafter controlling for SNP density, as described in the main text.

As XP-EHH and CLR both detect local deviations in the allele frequency spectrum (XP-EHHdetects regions of extended homozygosity), we expect them to largely overlap. This is indeed thecase for non-African populations–defining overlap as above, we find that the CLR and XP-EHHstatistics overlap 63%, 58%, 67%, 83%, 88%, and 71% for Europe, the Middle East, S. Asian, E.Asia, Oceania, and the Americas, respectively. For the Bantu, however, the overlap is only 28%.We interpret this to mean that many signals of fixed sweeps in the Bantu are less robust thanthose outside of Africa. This is consistent with the observation that there appear to be few reliablesignals of recent fixations in African populations[2, 4].

3

0 1 0 1 0 1

Derived allele frequency

Den

sity

AS

NY

RI

CE

U

Unascertained simulations Ascertained simulations Illumina

Figure 1: Marginal frequency spectra in the simulations before and after the application of theascertainment procedure, as well as in the real data. In the first column are the marginal allelefrequency spectra in the simulations before application of the ascertainment procedure, in thesecond column are the allele frequency spectra in the simulations after the application of theascertainment procedure, and in the third column are the marginal allele frequency spectra in theHapMap populations at the SNPs typed on the Illumina panel.

4

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Figure 2: Power of iHS (A) and XP-EHH (B) in three demographies based on theHapMap. Selected alleles were introduced at a random time with a selection coefficient of 1%and simulated forwards in time. In all simulations, the selected site was excluded from analyses.Simulations were binned into six bins according the the final frequency of the selected allele. Thetype I error was set to 1%, with the threshold determined by neutral simulations.

5

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Figure 3: Power of iHS (A) and XP-EHH (B) in the YRI demography for differentsample sizes (in number of chromosomes). Selected alleles were introduced at a random timewith a selection coefficient of 1% and simulated forwards in time. Simulations were binned into sixbins according the the final frequency of the selected allele. The type I error was set to 1%, withthe threshold determined by neutral simulations.

6

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Figure 4: Overlap of iHS signals across populations. In each cell (i, j) the fraction of windows withscores in the 1% tail of iHS in population i and in the 5% tail of iHS in population j is coloredaccording the legend on the right.

7

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8

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sia Oce

ania

Am

erica

0.0

5

0.0

01

Figure 6: Top 10 iHS (A) and XP-EHH (B) signals by population cluster. This isanalogous to Figure 1 in the main text, but uses a sliding window of 200kb that slides in steps of100kb.

9

chr9

31.

2:31

.6ch

r7 6

6.6:

67ch

r2 9

7.6:

97.8

COX5

B,AC

TR1B

,ZAP

70ch

r5 1

09:1

09.2

MAN

2A1

chr6

26.

4:26

.6BT

N3A2

,BTN

2A2,

BTN3

A1,B

TN2A

3,BT

N3A3

,BTN

2A1

chr3

29.

4:29

.8RB

MS3

chr1

1 57

.8:5

8O

R5B1

7,O

R5B3

,OR5

B2,O

R5B1

2ch

r3 1

33.2

:133

.4CP

NE4

chr6

85.

4:85

.6TB

X18

chr1

3 35

.4:3

5.6

DCAM

KL1

chr1

9 43

.4:4

3.6

DPF1

,PPP

1R14

A,SP

INT2

,LO

C541

469,

C19o

rf33,

YIF1

B,KC

NK6,

C19o

rf15,

PSM

D8,G

GN,

SPRE

D3,R

ASG

RP4,

FAM

98C

chr9

11.

8:12

chr1

1 10

9.8:

110.

2FD

X1,A

RHG

AP20

chr1

4 97

.6:9

7.8

chr1

0 20

.4:2

0.6

PLXD

C2ch

r11

9.8:

10.2

SBF2

chr9

99.

6:99

.8AN

P32B

,C9o

rf156

,FO

XE1,

HEM

GN

chr1

6 22

.8:2

3HS

3ST2

,USP

31ch

r4 1

19.8

:120

KIAA

1627

,SEC

24D

chr2

167

.6:1

68CM

YA3

chr1

7 60

.6:6

0.8

RGS9

chr9

107

:107

.2SL

C44A

1ch

r14

60.8

:61.

2TM

EM30

B,PR

KCH

chr4

60.

6:61

chr9

3.2

:3.4

RFX3

chr3

131

.4:1

31.8

FLJ3

5880

chr3

25.

8:26

OXS

Mch

r2 1

78:1

78.2

AGPS

,TTC

30A,

TTC3

0B,P

DE11

Ach

r2 2

12.8

:213

.2ER

BB4

chr4

34:

34.2

chr1

4 62

.6:6

3KC

NH5,

RHO

J,G

PHB5

,PPP

2R5E

chr5

19.

6:20

CDH1

8ch

r8 1

39.6

:139

.8CO

L22A

1ch

r15

27:2

7.2

APBA

2ch

r7 1

19.8

:120

.2KC

ND2

chr1

5 46

:46.

4SL

C24A

5,M

YEF2

,SLC

12A1

chr1

7 51

:51.

4TM

EM10

0,PC

TPch

r8 1

1:11

.2C8

orf1

5,M

TMR9

,XKR

6ch

r22

45:4

5.2

FLJ2

0699

,PPA

RA,L

OC1

5038

3,PK

DREJ

,GTS

E1,T

RMU,

CELS

R1ch

r10

83.8

:84.

2NR

G3

chr6

73.

8:74

KCNQ

5ch

r2 1

08.8

:109

FLJ3

2745

,EDA

Rch

r6 1

25.8

:126

.2HE

Y2,N

COA7

chr2

108

:108

.4SU

LT1C

3,SU

LT1C

1,SU

LT1C

2ch

r10

55.6

:55.

8PC

DH15

chr1

0 94

.8:9

5.2

EXO

C6,C

YP26

C1,C

YP26

A1,F

ER1L

3ch

r5 1

12.2

:112

.6AP

C,SR

P19,

DCP2

,MCC

,REE

P5ch

r10

55:5

5.2

chr1

1 25

.2:2

5.6

chr1

2 1.

2:1.

4ER

C1ch

r8 6

3.8:

64FA

M77

Dch

r3 6

7.6:

67.8

SUCL

G2

chr2

165

.2:1

65.6

COBL

L1,F

LJ39

822

chr2

126

:126

.2ch

r14

69.4

:69.

6SM

OC1

,SLC

8A3

chr5

61.

2:61

.4ch

r6 2

9.4:

29.6

OR5

V1,O

R12D

3,O

R12D

2,O

R11A

1,O

R10C

1,O

R2H1

,MAS

1Lch

r3 1

62.6

:162

.8LO

C131

149

chr1

2 92

.8:9

3ch

r2 1

65.8

:166

.2SC

N2A,

FAM

130A

2ch

r16

11:1

1.4

PRM

1,KI

AA03

50,S

OCS

1,TN

P2,P

RM3,

PRM

2,C1

6orf7

5ch

r2 1

61.2

:161

.6ch

r6 4

7.6:

47.8

GPR

115,

GPR

111,

CD2A

Pch

r10

110:

110.

2ch

r12

30.8

:31

TSPA

N11

chr6

122

.6:1

22.8

HSF2

chr1

3 87

.8:8

8.2

chr5

141

:141

.2C5

orf1

6,FC

HSD1

,CEN

TD3

chr4

68.

6:68

.8TM

PRSS

11F,

CHR4

15SY

T,TM

PRSS

11B

chr8

33.

4:33

.6FU

T10,

RBM

13,C

8orf4

1,RN

F122

,DUS

P26

Biak

aPyg

my

Bantu Eu

rope Mi

deas

tS.

Asia E.

Asia Oc

eania Am

erica

0.05

0.00

1chr1

1 3

4.3

:34.4

AB

TB

2

chr1

0 9

.6:9

.8chr1

9 5

6.8

:56.9

SIG

LE

C5

chr1

9 5

2.2

:52.4

GR

LF

1,N

PA

S1,T

ME

M160,S

AE

1

chr7

106.2

:106.3

PIK

3C

G

chr2

80.1

:80.2

CT

NN

A2

chr1

7 0

.6:0

.8C

17orf

25,R

NM

TL1,N

XN

,GE

MIN

4

chr1

1 2

9.9

:30

KC

NA

4

chr1

3 1

07.7

:107.8

TN

FS

F13B

chr6

164.6

:164.7

chr1

4 8

4.6

:84.7

chr2

0 3

4.9

:35

C20orf

117,C

20orf

118,S

AM

HD

1

chr1

3 2

4.2

:24.3

RN

F17

chr1

9 4

7:4

7.2

LY

PD

4,R

PS

19,A

RH

GE

F1,R

AB

AC

1,A

TP

1A

3,G

RIK

5,D

MR

TC

2,C

EA

CA

M3,C

D79A

chr2

59.1

:59.2

chr1

1 6

3:6

3.2

HR

AS

LS

5,L

GA

LS

12,R

AR

RE

S3,H

RA

SLS

2,H

RA

SLS

3,D

KF

ZP

564J0863

chr1

0 1

2.4

:12.5

CA

MK

1D

chr1

207.1

:207.2

chr2

0 1

6.4

:16.5

C20orf

23

chr1

7 6

0.6

:60.9

RG

S9

chr1

7 5

6.1

:56.4

BC

AS

3

chr1

5 4

6.2

:46.5

SLC

24A

5,M

YE

F2,S

LC

12A

1,D

UT

,FB

N1

chr1

7 5

6.2

:56.7

BC

AS

3

chr8

140:1

40.2

chr5

74.8

:75.1

CO

L4A

3B

P,P

OLK

,C5orf

37

chr1

0 6

5.4

:65.7

chr1

8 1

1.2

:11.3

chr9

90.1

:90.4

SP

IN1,C

9orf

121

chr2

2 4

5:4

5.2

FLJ20699,P

PA

RA

,LO

C150383,P

KD

RE

J,G

TS

E1,T

RM

U,C

ELS

R1

chr1

2 8

7.6

:87.9

chr1

4 6

2.8

:63.1

RH

OJ,G

PH

B5,P

PP

2R

5E

chr1

0 2

2.4

:22.7

CO

MM

D3,B

MI1

,SP

AG

6

chr1

5 4

6.6

:46.8

FB

N1

chr5

26.5

:26.7

chr2

1 1

6.7

:17

C21orf

34

chr1

7 5

0.9

:51.1

chr4

29.5

:29.7

chr3

176.7

:176.9

NA

ALA

DL2

chr7

119.6

:119.9

KC

ND

2

chr2

2 2

1.6

:21.8

RT

DR

1,G

NA

Z

chr1

1 2

5.3

:25.6

chr4

158.7

:159

chr1

5 6

1.6

:61.9

US

P3,F

BX

L22,H

ER

C1

chr2

177.2

:177.5

chr4

41.7

:41.9

SLC

30A

9,C

CD

C4

chr2

17.6

:17.9

VS

NL1,S

MC

6,F

LJ40869

chr2

1 1

6.3

:16.6

C21orf

34

chr6

105.2

:105.5

HA

CE

1

chr5

58.9

:59.2

PD

E4D

chr8

19.5

:19.8

ChG

n,IN

TS

10

chr1

2 6

5.7

:66

CA

ND

1

chr4

95.2

:95.5

SM

AR

CA

D1,P

GD

S

chr8

100.2

:100.5

VP

S13B

chr5

58.6

:58.8

PD

E4D

chr6

105.8

:106

PR

EP

chr1

0 5

9.2

:59.4

chr1

2 1

25.4

:125.6

chr2

177.9

:178.2

AG

PS

,TT

C30A

,TT

C30B

,PD

E11A

chr2

158.4

:158.6

AC

VR

1,U

PP

2

chr2

178.3

:178.6

PD

E11A

chr2

2 4

6.4

:46.7

FLJ46257

chr1

6 1

1.1

:11.4

PR

M1,K

IAA

0350,S

OC

S1,T

NP

2,P

RM

3,P

RM

2,C

16orf

75

chr4

158.2

:158.4

GLR

B,G

RIA

2

Bia

kaP

ygm

y

Bantu E

uro

pe

Mid

east

S.A

sia E.A

sia Oce

ania

Am

erica

0.0

5

0.0

01

Figure 7: Top 10 iHS (A) and XP-EHH (B) signals by population cluster. This isanalogous to Figure 1 in the main text, but uses a window size of 100kb.

10

chr10 106.6:106.8 SORCS3

chr2 81.8:82.2chr11 55:55.6 OR4C15,OR4C11,OR4P4,OR4C6,OR5D13,OR5D14,OR5L1,OR5D18,OR5L2,OR5D16,SPRYD5,OR5W2,OR5I1,OR10AG1,OR5F1,OR5AS1,OR4C16,OR4S2

chr7 117.6:118 ANKRD7,LSM8

chr11 61.2:61.4 C11orf11,C11orf9,C11orf10,FEN1,FADS1,FADS2,FADS3

chr7 106.6:107 HBP1,COG5,DUS4L,GPR22

chr5 75.4:75.6 SV2C

chr11 56:56.2 OR5M8,OR5M11,OR5M10,OR5M1,OR5AP2,OR5AR1

chr10 64.6:65 JMJD1C,REEP3

chr7 127.2:127.4 SND1

chr5 158.4:158.6 EBF1,FLJ31951

chr12 85.8:86.2chr2 50.8:51 NRXN1

chr1 113.6:114 MAGI3

chr20 17.4:17.6 PCSK2,BFSP1,DSTN,RRBP1

chr6 100.8:101 SIM1

chr19 47:47.6 POU2F2,LYPD4,RPS19,ARHGEF1,RABAC1,ATP1A3,GRIK5,ZNF574,DEDD2,ZNF526,GSK3A,ERF,PAFAH1B3,MGC70924,MEGF8,C19orf49,CNFN,LIPE,CIC,TMEM145,DMRTC2,CEACAM3,CD79A

chr14 62.8:63 RHOJ,GPHB5,PPP2R5E

chr13 33:33.4 RFC3

chr15 67.4:67.8 PAQR5,KIF23,RPLP1,LOC729416

chr3 190:190.4 LPP,FAM79B

chr5 11.6:12 CTNND2

chr5 109.6:110.2 SLC25A46

chr6 128.6:129 PTPRK

chr2 21.4:21.8chr18 30.4:30.6 DTNA

chr13 103.6:103.8chr1 35.2:36 SFPQ,ZMYM4,KIAA0319L,NCDN,TFAP2E,PSMB2,FLJ38984,CLSPN,ZMYM1,ZMYM6

chr15 46:46.4 SLC24A5,MYEF2,SLC12A1

chr8 24:24.4 ADAM7,ADAM28,ADAMDEC1

chr12 87.4:88 KITLG

chr5 111.6:111.8 EPB41L4A

chr21 16.6:17 C21orf34

chr3 98.4:98.8 EPHA6

chr9 32.6:32.8 TAF1L,LOC401498

chr17 55.6:56.4 USP32,C17orf64,APPBP2,PPM1D,BCAS3

chr7 119.4:120 KCND2

chr5 117.4:117.8chr4 41.4:42 PHOX2B,TMEM33,WDR21B,SLC30A9,CCDC4

chr2 177.2:177.6chr3 108.6:109.2 BBX

chr15 61.6:62.2 USP3,FBXL22,HERC1,DAPK2,FAM96A,SNX1

chr8 10.8:11.2 C8orf15,MTMR9,XKR6

chr1 103.2:103.6 COL11A1

chr3 25.6:26.2 RARB,TOP2B,NGLY1,OXSM

chr8 138.8:139.2chr8 63.2:64.4 YTHDF3,FAM77D,GGH,TTPA,FLJ39198

chr4 159.2:160 C4orf18,TMEM144,RXFP1,LOC201725,PPID,ETFDH

chr10 44:44.2 CXCL12

chr5 58.8:59.2 PDE4D

chr2 151.6:152 RBM43,NMI,TNFAIP6,RIF1

chr10 110.2:111.2chr4 160.2:160.6

chr9 0.8:1 DMRT1,DMRT3

chr8 9.8:10.2 MSRA

chr4 170.4:171.2 SH3RF1,NEK1,CLCN3,C4orf27,MFAP3L

chr10 59.2:59.6chr2 177.8:178.4 PDE11A,NFE2L2,AGPS,TTC30A,TTC30B

chr1 50.8:51.6 C1orf34,FAF1,CDKN2C,RNF11,EPS15

chr6 122:122.4chr2 158.8:159.4 LOC130940,PKP4,LOC92196

chr3 157.4:157.8 KCNAB1,SSR3

chr6 35.2:35.6 TCP11,SCUBE3,ZNF76,DEF6,FANCE,RPL10A,TEAD3,TULP1,PPARD

chr12 125.4:125.8chr6 49.4:49.8 MUT,CENPQ,C6orf141,RHAG,CRISP2

chr5 155:155.4

BiakaPygmy

BantuEurope

Mideast

S.AsiaE.Asia

Oceania

America

0.05

0.001

Figure 8: Top 10 CLR signals by population cluster. This is analogous to Figure 1 in themain text.

11

Africa−Europe

Cou

nts

040

080

012

00

AB CDEF GHIJ K LMNOP QRS

Africa−E.Asia

Cou

nts

040

080

012

00

A BC DEF GHI J K LMN O PQRS

Europe−E.Asia

Cou

nts

050

010

0015

00

ABCDEFGHIJ KL MNOP QR S

S.Asia−E.AsiaC

ount

s

050

015

00

ABCDEFGHIJ KLMNOP QR S

Africa−S.Asia

FST

Cou

nts

050

010

0015

00

0.0 0.2 0.4 0.6 0.8 1.0

A BCDEF GHI J KLMNOP QRS

Europe−S.Asia

FST

Cou

nts

050

015

00

0.0 0.2 0.4 0.6 0.8 1.0

AB CDEFGHIJKLMNOP QRS

Fst

Cou

nts

ABCDEFGHIJ

CETPLPLLIPCABCA1LIPGAPOC_clustAPOBLDLRAPOA_clustGCKR

KLMNOPQRS

LPL_2

SORT1PDSK9GALNT2MVKNCANTRIB1MLXIPLANGPTL3

Figure 9: FST surrounding loci involved in natural variation in lipid levels. This figurewas generated as in Figures 3 and 4 in the main text.

12

Africa−Europe

Cou

nts

040

080

012

00

A BCD E FG HI JKL MNOP QRST UVWXY Z1 234

Africa−E.Asia

Cou

nts

040

080

012

00

ABCD EF GHIJK LM NOPQRS TUVW XYZ 12 34Europe−E.Asia

Cou

nts

050

010

0015

00

AB CDEFGHI JK LM NOPQRS TUVWXY Z123 4

S.Asia−E.AsiaC

ount

s

050

015

00

AB CDE F GHI JK LM NOP QRS TUVWXYZ12 3 4

Africa−S.Asia

FST

Cou

nts

050

010

0015

00

0.0 0.2 0.4 0.6 0.8 1.0

ABCD EFG HI JKLMN OP QRSTUVWXY Z1 234

Europe−S.Asia

FST

Cou

nts

050

015

00

0.0 0.2 0.4 0.6 0.8 1.0

ABCD EFGHI JKLMNOPQRSTUVWXYZ1234

Fst

Cou

nts

ABCDEFGHIJ

IL23RATG16L1MST1PTGER45q31IRGMTNFSF15ZNF365NKX2−3NOD2

KLMNOPQRST

PTPN2PTPN22ITLN11q241q32IL12BCDKAL16q21CCR67p12

UVWXYZ1234

8q24JAK210p11C11orf30LRKK213q14ORMDL3STAT321q21ICOSLG

Figure 10: FST surrounding loci involved in natural variation in susceptibility to Crohn’sdisease. This figure was generated as in Figures 3 and 4 in the main text.

13

Africa−Europe

FST

Cou

nts

040

080

012

00

ABC D EF GHI J KLMNO PQR ST UVWXYZ1 2345678 9 abcdef gh

Africa−E.Asia

Cou

nts

040

080

012

00

AB CDE FGHI J KLMNOPQ R ST UVW X YZ1 23 456 789 abcd efg h

Europe−E.Asia

Cou

nts

050

010

0015

00

ABCDE FGHI JKLMNO PQRSTU VWXYZ12 3 45 67 8 9a bcd efgh

S.Asia−E.AsiaC

ount

s

050

015

00

A BCDE FGHI JKLM NOPQR STU VWXYZ12 345 678 9a bcd efghAfrica−S.Asia

FST

Cou

nts

050

010

0015

00

0.0 0.2 0.4 0.6 0.8 1.0

ABCD EFG HI J KLMNOP QR ST UVWXYZ1 2345 6789 abcdefgh

Europe−S.Asia

FST

Cou

nts

050

015

00

0.0 0.2 0.4 0.6 0.8 1.0

ABCDEFGHIJK LMNO PQRSTUVWXYZ 123456789abcdef gh

Fst

Cou

nts

ABCDEFGHIJKLMNO

ZBTB38CDK6HMGA2GDF5LCORLLOC387103EFEMP1C6orf106PTCH1SPAG17SOCS2HHIPZNF678DLEU7SCMH1

PQRSTUVWXYZ1234

ADAMTSL3IHHCEP63ACANDYM1q12DNM3C1orf19BMP66p22BAT3TNXB6p21EGPR126GNA12

5

6

7

8

9a

bc

de

fg

h

PLAG18q21

ZNF46214q32

ADAMTS1717q11

17q23A

17q23B

18q11

BMP2

LIN28B

DOTL1

CDCHD7

Figure 11: FST surrounding loci involved in natural variation in height. This figure wasgenerated as in Figures 3 and 4 in the main text.

14

Pygmy−Bantu

FST

Cou

nts

050

010

0015

0020

0025

00

0.0 0.2 0.4 0.6 0.8 1.0

ABC D

EFG H

I JK

LM

NO

PQ RS TU VWX

YZ12

345 67

89abc

d

ef

gh

A

B

C

D

E

F

G

H

I

J

K

L

M

N

O

ZBTB38

CDK6

HMGA2

GDF5

LCORL

LOC387103

EFEMP1

C6orf106

PTCH1

SPAG17

SOCS2

HHIP

ZNF678

DLEU7

SCMH1

P

Q

R

S

T

U

V

W

X

Y

Z

1

2

3

4

ADAMTSL3

IHH

CEP63

ACAN

DYM

1q12

DNM3

C1orf19

BMP6

6p22

BAT3

TNXB

6p21E

GPR126

GNA12

5

6

7

8

9

a

b

c

d

e

f

g

h

PLAG1

8q21

ZNF462

14q32

ADAMTS17

17q11

17q23A

17q23B

18q11

BMP2

LIN28B

DOTL1

CDCHD7

Figure 12: FST between Bantu and Pygmy populations surrounding loci involved innatural variation in height. This figure was generated as in Figures 3 and 4 in the main text.

15

chr19 43.4:43.6 RYR1,SIPA1L3,DPF1,PPP1R14A,SPINT2,LOC541469,C19orf33,YIF1B,KCNK6,C19orf15,PSMD8,GGN,SPRED3,RASGRP4,FAM98C

chr9 11.8:12chr11 109.8:110.2 FDX1,ARHGAP20

chr14 97.6:97.8chr13 87.8:88

chr10 20.4:20.6 PLXDC2

chr11 9.8:10.2 SBF2

chr9 99.6:99.8 ANP32B,C9orf156,FOXE1,HEMGN

chr16 22.8:23 HS3ST2,USP31

chr4 119.8:120 KIAA1627,SEC24D,SYNPO2

chr4 119.2:119.6 NDST3,PRSS12

chr5 109:109.2 MAN2A1

chr3 4.4:4.6 SUMF1,ITPR1

chr1 200.8:201 PPP1R12B,SYT2,JARID1B

chr19 56.6:56.8 ETFB,CLDND2,NKG7,LIM2,SIGLEC12,SIGLEC6,ZNF175,SIGLEC5,SIGLEC10,SIGLEC8,LOC729767

chr2 155.4:155.6 KCNJ3

chr8 49.2:49.4chr8 140.2:140.4

chr20 46.6:47 PREX1,ARFGEF2

chr3 165.4:165.6chr12 78:78.2 SYT1

chr22 34.2:34.4 MCM5,RASD2,MB,LOC284912,APOL6,APOL5

chr6 100.8:101 SIM1

chr3 165:165.2chr9 114:114.2 SUSD1,ROD1,HSDL2

chr16 80:80.2 GAN,CMIP

chr2 12.2:12.4chr12 81.4:81.6 C12orf26,TMTC2

chr17 3.4:3.6 TRPV1,CTNS,TRPV3,CARKL,TAX1BP3,TMEM93,P2RX5,ITGAE,GSG2

chr7 20.4:20.6 ITGB8

chr13 29.4:29.6 LOC440131

chr12 28:28.2 PTHLH

chr4 163:163.2 FSTL5

chr11 112.4:112.6 NCAM1

chr7 156.2:156.4 RNF32,LMBR1,NOM1

chr9 28.6:28.8 LINGO2

chr18 40.8:41.2 SETBP1

chr14 31.2:31.4 NUBPL

chr9 138.8:139 MAMDC4,LCN10,LCN6,LCN8,UNQ2541,TMEM141,C9orf86,PHPT1,EDF1,TRAF2,FBXW5,C8G,PTGDS,FLJ45224,C9orf142,CLIC3,ABCA2,C9orf139,FUT7,KIAA1984,LCN12,LOC389813

chr8 21.2:21.4chr11 6:6.2 OR52L1,OR56A1,OR56B4,OR52B2,OR52W1,C11orf42,C11orf56,CNGA4,CCKBR,OR56A4

chr8 113.8:114 CSMD3

chr9 94.6:94.8 ANKRD19,BICD2,ZNF484,FGD3

chrX 137.8:138chr6 130.6:130.8 SAMD3,KIAA1913

chr3 100.8:101 COL8A1,FLJ44076,C3orf26,FILIP1L

chr4 139:139.2chr9 24:24.2

chr18 42.2:42.4 RNF165,LOXHD1

chr6 72.8:73 RIMS1

chr9 110.8:111 EPB41L4B,C9orf4,C9orf5,CTNNAL1

chr13 57:57.2 PCDH17

chr13 56.4:56.6 FLJ40296

chr9 114.6:114.8 TSCOT,ZFP37

chr3 56.6:56.8 CCDC66,C3orf63,ARHGEF3

chr18 64.8:65 CCDC102B

chr11 83.8:84 DLG2

chr22 34.8:35 APOL3,APOL4,APOL2,APOL1,MYH9

chr4 34.2:34.4chr6 77:77.2

chr11 87.4:87.6 RAB38

chr3 118.4:118.6chr5 66.8:67.2

chr3 46:46.2 FYCO1,CXCR6,XCR1,CCR1

chr12 80.6:80.8 PPFIA2

chr16 25.8:26 HS3ST4

chr11 40.4:40.6chr3 61:61.2 FHIT

chr6 26.4:26.6 HIST1H4G,HIST1H3F,HIST1H2BH,HIST1H3G,HIST1H2BI,HIST1H4H,BTN3A2,BTN2A2,BTN3A1,BTN2A3,BTN3A3,BTN2A1,BTN1A1,HMGN4

chr1 79.6:79.8chr5 43:43.2 AXIIR,ZNF131,MGC42105

chr21 29.4:29.6 CCT8,C21orf7,BACH1

chr6 29.6:29.8 MAS1L,OR2H2,GABBR1,MOG,HLA−F

chr2 98.2:98.4 INPP4A,MGC26733,CNGA3

chr7 92:92.2 MGC40405,CDK6,DKFZP564O0523,PEX1

chr15 54.2:54.4 RFXDC2,TEX9

chr1 79:79.2chr7 82.6:82.8 SEMA3E

chr7 141:141.2 AGK,FLJ40852,SSBP1,TAS2R3,TAS2R4,TAS2R5,LOC136242,KIAA1147

chr14 71.8:72 RGS6

chr1 173.4:173.6 TNN,KIAA0040,TNR

chr8 5.2:5.4chr4 130.2:130.4 SCLT1,C4orf33

chr3 76.8:77chr1 88.8:89 PKN2

chr5 162:162.2chr9 76:76.2chr8 9.2:9.4

chr21 43:43.2 PDE9A,WDR4,NDUFV3

chrX 125:125.2 WDR40C

chr10 90.2:90.4 C10orf59,LIPL1,LIPF

chr8 68.8:69 CPA6,DEPDC2

chr6 70.6:70.8 LMBRD1,COL19A1

chr9 81:81.2chr6 75.4:75.6

chr5 145.8:146 TCERG1,GPR151,PPP2R2B

chr5 163.4:163.6chr17 42.6:42.8 CDC27,MYL4,ITGB3,C17orf57

chr15 59.8:60 VPS13C

chr21 44.8:45 C21orf29,KRTAP10−1,KRTAP10−2,KRTAP10−3,KRTAP10−4,KRTAP10−5,KRTAP10−6,KRTAP10−7,KRTAP10−8,KRTAP10−9,KRTAP10−10,KRTAP10−11,KRTAP12−4,KRTAP12−3,KRTAP12−2,KRTAP12−1,KRTAP10−12,UBE2G2,SUMO3

chr10 58:58.2chr12 5.2:5.4

chr2 86.6:86.8 JMJD1A,VPS24,RNF103,RMND5A

chr10 68.8:69 CTNNA3

chr15 74.4:74.6 ISL2,ZNF291,ETFA

BiakaPygmy

BantuEurope

Mideast

S.AsiaE.Asia

Oceania

America

0.05

0.001

Figure 13: The top 1% of iHS signals in the Bantu, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.

16

chr9 31.2:31.6chr7 66.6:67

chr2 97.6:97.8 COX5B,ACTR1B,ZAP70,KIAA1641

chr5 109:109.2 MAN2A1


chr3 29.4:29.8 RBMS3

chr11 57.8:58 OR10Q1,OR10W1,OR5B17,OR5B3,OR5B2,OR5B12,OR5B21

chr3 133.2:133.4 CPNE4

chr6 85.4:85.6 TBX18

chr13 35.4:35.6 DCAMKL1,SOHLH2

chr2 99.6:99.8 AFF3

chr9 86:86.2 SLC28A3

chr9 75.2:75.4chr15 53.8:54 PRTG,NEDD4

chr3 75:75.2chr15 54.8:55 SUHW4,TCF12

chr9 13.6:13.8chr12 70.6:70.8 TBC1D15,TPH2

chr15 55.2:55.4 TCF12

chr2 55:55.2 RTN4,FLJ42562

chr4 160.8:161.2chr5 130:130.2

chr3 155.2:155.4 SGEF

chr1 5:5.2chr16 11:11.2 KIAA0350

chr2 173:173.2 ITGA6,PDK1

chr7 28.6:28.8 CREB5

chr19 36.6:36.8chr10 19:19.2 NSUN6,ARL5B

chr3 27.2:27.4 NEK10,SLC4A7

chr7 29.8:30 SCRN1,FKBP14,PLEKHA8,WIPF3

chr7 40.6:40.8 C7orf10

chr5 123:123.2 CSNK1G3

chr18 40.8:41 SETBP1

chr20 57.6:57.8 PHACTR3

chr2 43.6:43.8 THADA,PLEKHH2

chr10 67.4:67.6 CTNNA3

chr2 84.6:84.8 FLJ37357

chr7 84.2:84.4chr11 16.4:16.6 SOX6

chr11 76.6:76.8 GDPD4,PAK1,MYO7A

chr18 19.2:19.4 RIOK3,C18orf8,NPC1,ANKRD29,C18orf45

chr3 20:20.2 C3orf48,EFHB,RAB5A,PCAF,SGOL1

chr10 3:3.2 PFKP,PITRM1

chr1 189.8:190chr13 57.4:57.6chr5 14.2:14.4 TRIO

chr7 9.4:9.6chr5 26.6:26.8chr2 42.2:42.4 EML4,COX7A2L

chr2 229.8:230 DNER,PID1

chr5 136.2:136.4 SPOCK1

chr2 46.4:46.6 EPAS1,ATP6V1E2,RHOQ

chr2 84.2:84.4 LOC388965

chr2 98.2:98.4 INPP4A,MGC26733,CNGA3

chr6 23.8:24chr6 115.8:116

chr6 154.2:154.4 OPRM1

chr7 125.4:125.6chr11 73.6:73.8 DKFZP586P0123,PPME1,P4HA3,PGM2L1,KCNE3

chr15 42.8:43 B2M,TRIM69,C15orf43

chr2 50.2:50.4 NRXN1

chr15 51.2:51.4chr6 159.8:160.2 SOD2,WTAP,ACAT2,TCP1,MRPL18,PNLDC1,MAS1

chr6 19:19.2chr7 2.8:3 GNA12,CARD11

chr15 97.4:97.6 TTC23,LRRC28,DMN

chr2 209.8:210 MAP2

chr5 140.8:141 PCDHGA1,PCDHGA2,PCDHGA3,PCDHGB1,PCDHGA4,PCDHGB2,PCDHGA5,PCDHGB3,PCDHGA6,PCDHGA7,PCDHGB4,PCDHGA8,PCDHGB5,PCDHGA9,PCDHGB6,PCDHGA10,PCDHGB7,PCDHGA11,PCDHGA12,PCDHGC3,PCDHGC4,PCDHGC5,HDAC3,C5orf16,FCHSD1,CENTD3,DIAPH1

chr15 63.2:63.4 PDCD7,CLPX,CILP,PARP16,PUNC

chr3 76.8:77chr3 3.6:3.8 LRRN1

chr5 108.4:108.6 FER

chr6 131.2:131.4 EPB41L2

chr5 18.2:18.4chr13 90.4:90.6

chr3 63:63.2chr20 37.8:38

chr5 135.4:135.6 TGFBI,SMAD5,TRPC7

chr14 64.8:65 FUT8

chr14 80.4:80.6 C14orf145,TSHR

chr9 114.6:114.8 TSCOT,ZFP37

chrX 145.6:145.8chr2 25.2:25.4 POMC,DNMT3A

chr22 31.6:31.8 SYN3,TIMP3

chr8 69.6:69.8 C8orf34

chr1 5.8:6 NPHP4,KCNAB2

chr11 38.4:38.6chr11 104.6:104.8

chr1 79:79.2chr21 40.8:41 DSCAM


chr4 130.2:130.4 SCLT1,C4orf33

chr5 160.2:160.4chr16 78.6:78.8

chr5 129.2:129.4 CSS3

chr6 56:56.2 COL21A1

chr18 60.2:60.4chr6 2.2:2.4 GMDS

chr6 133:133.2 TAAR2,TAAR5,TAAR1,VNN1,VNN3,VNN2,C6orf192,RPS12

chr10 119.4:119.6

BiakaPygmy

BantuEurope

Mideast

S.AsiaE.Asia

Oceania

America

0.05

0.001

Figure 14: The top 1% of iHS signals in the Biaka Pygmies, ordered from top to bottom in orderof significance. See the caption of Figure 1 in the main text for details.

17

chr2 167.6:168 CMYA3

chr17 60.6:60.8 RGS9

chr9 107:107.2 SLC44A1

chr14 60.8:61.2 TMEM30B,PRKCH,HIF1A

chr5 112.4:112.6 DCP2,MCC

chr4 60.6:61chr9 3.2:3.4 RFX3

chr3 131.4:131.8 FLJ35880

chr3 25.8:26 NGLY1,OXSM

chr2 178:178.2 PDE11A,AGPS,TTC30A,TTC30B

chr8 52.6:53 PCMTD1

chr8 139.6:139.8 C8ORFK32,COL22A1

chr7 119.8:120.2 KCND2,TSPAN12

chr6 30:30.4 HLA−A,HCG9,ZNRD1,RNF39,TRIM31,TRIM40,TRIM15,TRIM26,FLJ45422,TRIM39,RPP21,PPP1R11

chr18 19.6:19.8 LAMA3,C18orf17

chr2 197.4:197.6 GTF3C3,UNQ6411,PGAP1,ANKRD44

chr5 145.8:146.2 TCERG1,GPR151,PPP2R2B

chr8 140:140.2 COL22A1

chr15 91.8:92chr5 21.8:22 CDH12

chr2 158.2:158.6 ACVR1C,ACVR1,UPP2

chr2 195.4:195.6chr15 67.2:67.4 GLCE,PAQR5

chr6 105.8:106 PREP

chr9 12.4:12.8 TYRP1,C9orf150

chr4 34:34.2chr10 83.6:83.8 NRG3

chr5 74.6:74.8 HMGCR,COL4A3BP,POLK

chr16 80.8:81 MPHOSPH6

chr4 186.4:186.6 SNX25,LRP2BP,ANKRD37,C4orf20,CCDC110


chr9 125.4:125.6 DENND1A

chr5 142:142.4 FGF1,ARHGAP26

chr12 40:40.2 PDZRN4

chr7 36.8:37.2 ELMO1

chr4 148.4:148.6 EDNRA

chr1 65.2:65.4 AK3L1,AK3L2,JAK1

chr18 7.4:7.6 PTPRM

chr1 160.2:160.6 ATF6,OLFML2B,NOS1AP,C1orf111,SH2D1B

chr21 29.8:30 GRIK1

chr4 32.6:32.8chr12 101:101.2 CCDC53,NUP37,PMCH,C12orf48

chr2 238:238.2 COL6A3,PRLH,RAB17,MLPH

chr10 84:84.2 NRG3

chr12 110.2:110.4 FAM109A,SH2B3,ATXN2,CUTL2

chr1 244:244.2 SMYD3

chr5 23.2:23.4chr18 24.8:25

chr6 24.2:24.4 NRSN1,DCDC2

chr8 30:30.2 TMEM66,LEPROTL1,DCTN6

chr9 86.4:86.6 NTRK2

chr10 115:115.2chr7 19.2:19.4 FERD3L

chr4 29.8:30chr17 51.2:51.4 TMEM100,PCTP

chr16 78.2:78.6 MAF

chr9 93.2:93.4 AUH,NFIL3

chr2 40.2:40.4 SLC8A1

chr15 85.2:85.4 AGBL1

chr1 11.4:11.6 FBXO2,FBXO44,FBXO6


chr15 27:27.2 APBA2

chr11 20.8:21 NELL1

chr2 123:123.2chr5 24.6:24.8 CDH10

chr14 63.4:63.6 SYNE2

chrX 24:24.2 KLHL15,EIF2S3,ZFX

chrX 93.2:93.4chr6 30.6:30.8 IER3,PRR3,HLA−E,GNL1,ABCF1,PPP1R10,MRPS18B,C6orf134,C6orf136,DHX16,NRM,MDC1,TUBB,FLOT1

chr4 41.2:41.6 DKFZP686A01247,PHOX2B,TMEM33

chr3 72.6:72.8 RYBP

chr3 100.6:100.8 COL8A1

chr13 18.6:18.8 TUBA3C

chr4 14.2:14.4chr5 38:38.2

chr12 61:61.2 USP15,MON2

chr17 9.4:9.6 WDR16,STX8,USP43

chr9 130:130.2 LCN2,CIZ1,DNM1,GOLGA2,TRUB2,COQ4,SLC27A4,URM1,CEECAM1,C9orf16

chr12 11.4:11.6 PRB4,PRB1,PRB2

chr11 87.2:87.4chr12 123.2:123.4 NCOR2,FAM101A

chr7 7.2:7.4 C1GALT1,COL28A1

chr16 76.8:77 WWOX

chr2 147.4:147.6chr8 52:52.2

chr16 1.6:1.8 MAPK8IP3,IFT140,CRAMP1L,HN1L,NME3,MRPS34,EME2,SPSB3,NUBP2,IGFALS,FAHD1,C16orf73,HAGH

chr22 30.2:30.4 DRG1,EIF4ENIF1,SFI1,PISD,C22orf30

chr6 102.2:102.4 GRIK2

chr6 167.2:167.4 RPS6KA2,RNASET2,FGFR1OP

chr5 115.6:115.8 COMMD10,SEMA6A

chr3 103.6:103.8 ZPLD1

chr17 74.4:74.6 TIMP2,LGALS3BP,CANT1,C1QTNF1,FLJ21865

chr2 196.6:196.8 DNAH7,STK17B,HECW2

BiakaPygmy

BantuEurope

Mideast

S.AsiaE.Asia

Oceania

America

0.05

0.001

Figure 15: The top 1% of iHS signals in the Europeans, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.

18

chr9 107:107.2 SLC44A1

chr2 212.8:213.2 ERBB4

chr4 34:34.2chr14 62.6:63 KCNH5,RHOJ,GPHB5,PPP2R5E

chr5 19.6:20 CDH18

chr8 139.6:139.8 C8ORFK32,COL22A1

chr17 60.6:60.8 RGS9

chr15 27:27.2 APBA2



chr18 64.8:65 CCDC102B

chr10 84:84.4 NRG3

chr20 21.2:21.4 C20orf19,XRN2,NKX2−2

chr12 40:40.4 PDZRN4

chr9 125.2:125.6 CRB2,DENND1A

chr14 61:61.2 PRKCH,HIF1A

chr21 29.6:30 BACH1,GRIK1

chr22 45:45.2 FLJ20699,PPARA,LOC150383,PKDREJ,GTSE1,TRMU,CELSR1

chr1 244:244.2 SMYD3

chr1 65:65.2 RAVER2,JAK1


chr8 116.8:117 TRPS1

chr8 140:140.2 COL22A1

chr12 124.6:124.8 TMEM132B


chr5 30.6:30.8chr11 129.4:129.6 PRDM10,C11orf37,APLP2,ST14,ZBTB44

chr6 108:108.2 SCML4,FLJ10159


chr4 60.6:61chr5 142:142.4 FGF1,ARHGAP26

chr10 22.4:22.6 COMMD3

chr3 131.6:131.8 FLJ35880

chr5 110.2:110.4 TSLP

chr3 113:113.2 TMPRSS7,PLCXD2,PHLDB2,ABHD10,TAGLN3

chr12 125.6:125.8chr2 72.2:72.4 CYP26B1

chr7 33.6:33.8 BBS9

chr15 67.4:67.6 GLCE,PAQR5,KIF23,RPLP1,LOC729416

chr16 1.6:1.8 MAPK8IP3,IFT140,CRAMP1L,HN1L,NME3,MRPS34,EME2,SPSB3,NUBP2,IGFALS,FAHD1,C16orf73,HAGH

chr16 77:77.2 WWOX

chr12 98.2:98.4 ANKS1B

chr12 10:10.4 FLJ46363,CLEC12A,CLEC1B,CLEC12B,CLEC9A,CLEC1A,CLEC7A,GABARAPL1,KLRD1,KLRK1,C12orf59,OLR1

chr2 195.4:195.6chrX 19:19.2 GPR64

chr22 48.6:48.8 MLC1,BRD1,ZBED4,ALG12,CRELD2,PIM3,FLJ41993,LOC164714

chr20 22.2:22.6 FOXA2

chr17 59.6:59.8 ERN1,TEX2,PECAM1

chr3 64.2:64.4 PRICKLE2

chr14 63.4:63.6 SYNE2

chr12 87.2:87.4 KITLG

chr20 48.8:49 PARD6B,BCAS4,ADNP,DPM1,MOCS3

chr8 52.8:53 PCMTD1

chr4 170.2:170.6 CBR4,SH3RF1,NEK1

chr11 83.4:83.6 DLG2

chr13 73.8:74chr4 29.8:30

chr14 23.8:24 C14orf124,TGM1,CHMP4A,MDP−1,NEDD8,GMPR2,TINF2,RABGGTA,DHRS1,C14orf21,LTB4R2,LTB4R,ADCY4,NFATC4,KIAA0323,CMA1,RIPK3,CIDEB,CBLN3

chr2 1.8:2 MYT1L

chr17 51:51.2 TMEM100,PCTP

chr1 212.4:212.6 SMYD2,PTPN14

chr10 83.6:83.8 NRG3

chr15 91.8:92chr1 246.2:246.4 OR2T8,OR2L13,OR2L8,OR2AK2,OR2L2,OR2L3,OR2M5,OR2M2,OR2M3

chr2 21.6:21.8chr8 116:116.2

chr13 103:103.2chr5 21.8:22 CDH12

chr4 148.4:148.6 EDNRA

chr7 124.2:124.4 POT1,GPR37,LOC401398

chr8 55.2:55.4 LYPLA1,MRPL15

chr20 52.6:52.8 DOK5

chr11 17.6:17.8 MYOD1,SERGEF,KCNC1

chr4 43:43.2chr5 92.4:92.6

chr2 152.2:152.4 NEB,ARL5A,CACNB4

chr5 24.6:24.8 CDH10

chr6 30:30.4 HLA−A,HCG9,ZNRD1,RNF39,TRIM31,TRIM40,TRIM15,TRIM26,FLJ45422,TRIM39,RPP21,PPP1R11

chr12 110.2:110.4 FAM109A,SH2B3,ATXN2,CUTL2

chr4 14.2:14.4chr17 72.2:72.4 ST6GALNAC1,MXRA7,SFRS2,MFSD11,MGAT5B,PTDSR,LOC124512

chr4 5.2:5.4 STK32B

chr5 115.6:115.8 COMMD10,SEMA6A

chr20 54:54.2 CBLN4

chr12 65.8:66 CAND1

chrX 33.8:34chr6 54.8:55 FAM83B

chr3 88:88.2 HTR1F,CGGBP1

chr8 84.6:84.8chr7 125.8:126 GRM8

chr4 130:130.2 PHF17,SCLT1,C4orf33

chr5 112.4:112.6 DCP2,MCC

chr15 64.8:65 SMAD6

chr18 7.4:7.6 PTPRM

chr5 74.6:74.8 HMGCR,COL4A3BP,POLK

chr8 42.6:42.8 CHRNA6,THAP1,RNF170,CHRNB3

chr15 46:46.2 SLC24A5,MYEF2

BiakaPygmy

BantuEurope

Mideast

S.AsiaE.Asia

Oceania

America

0.05

0.001

Figure 16: The top 1% of iHS signals in the Middle East, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.

19

chr15 46:46.4 SLC24A5,MYEF2,SLC12A1,DUT

chr17 51:51.4 TMEM100,PCTP


chr14 62.6:63 KCNH5,RHOJ,GPHB5,PPP2R5E

chr8 11:11.2 C8orf15,MTMR9,AMAC1L2,XKR6


chr10 83.8:84.2 NRG3


chr6 73.8:74 C6orf148,KCNQ5

chr8 139.6:139.8 C8ORFK32,COL22A1


chr6 30.2:30.6 PRR3,RNF39,TRIM31,TRIM40,TRIM15,TRIM26,FLJ45422,TRIM39,RPP21,HLA−E,GNL1,ABCF1

chr9 122.6:123 FBXW2,PSMD5,PHF19,TRAF1,C5,CEP110,RAB14

chr3 131.6:131.8 FLJ35880

chr2 237.2:237.4 CXCR7

chr1 234.8:235 LGALS8,HEATR1,ACTN2,MTR

chr9 107:107.2 SLC44A1

chr21 29:29.2 N6AMT1,ZNF294

chr4 34:34.4chr20 15.6:15.8 C20orf133


chr2 231.4:231.6 GPR55,CAB39,ITM2C,PSMD1

chr9 130:130.2 LCN2,CIZ1,DNM1,GOLGA2,TRUB2,COQ4,SLC27A4,URM1,CEECAM1,C9orf16

chr6 105.6:106 LIN28B,BVES,POPDC3,PREP

chr4 29.6:30chr5 117.4:117.6

chr15 27:27.2 APBA2


chr17 60.6:60.8 RGS9

chr3 142.2:142.4 SLC25A36,SPSB4,ACPL2

chr4 41.4:41.6 DKFZP686A01247,PHOX2B,TMEM33

chr18 64.8:65 CCDC102B

chr5 112.4:112.6 DCP2,MCC

chr2 218.8:219 GPBAR1,PNKD,ARPC2,TMBIM1,MGC50811,SLC11A1,CTDSP1,VIL1,USP37,AAMP

chr12 81.8:82 TMTC2

chr8 21.8:22 NUDT18,DOK2,XPO7,NPM2,FGF17,EPB49,RAI16,HR

chr21 16.2:16.4 USP25,C21orf34

chr7 86.4:86.6 KIAA1324L,DMTF1

chr3 25.4:25.6 RARB,TOP2B

chr16 78.4:78.6chr2 223.4:223.8 ACSL3,KCNE4

chr12 98.2:98.4 ANKS1B

chrX 66.4:66.6chr14 64.2:64.6 PLEKHG3,SPTB,CHURC1,GPX2,RAB15,FNTB,MAX


chr5 25:25.2chr9 86.4:86.6 NTRK2

chr13 67:67.2chr8 52.6:53 PCMTD1

chr3 66.8:67chr8 92:92.2 EFCBP1,TMEM55A,OTUD6B

chr11 129.4:129.6 PRDM10,C11orf37,APLP2,ST14,ZBTB44

chr9 93.6:93.8 ROR2,SPTLC1


chr8 10.6:10.8 RP1L1,C8orf74,SOX7,PINX1,XKR6

chr8 42.6:42.8 CHRNA6,THAP1,RNF170,CHRNB3

chr10 59.4:59.8 IPMK,ZCD1,UBE2D1,TFAM

chr21 29.4:29.8 CCT8,C21orf7,BACH1,GRIK1

chr7 37:37.2 ELMO1

chr11 113.4:113.6 HTR3A,ZBTB16

chr22 33.6:33.8 ISX

chr5 38:38.2chr12 79.2:79.4 C12orf64

chr4 180.2:180.4chr13 103:103.2chr4 173.8:174 GALNT17

chr4 170.2:170.4 CBR4,SH3RF1

chr14 63.4:63.6 SYNE2

chr15 64.8:65 SMAD6

chr13 74:74.2chr9 32.6:32.8 NDUFB6,TAF1L,LOC401498

chr2 196.6:196.8 DNAH7,STK17B,HECW2

chr20 9.4:9.6 PLCB4,C20orf103,PAK7

chr12 18.8:19 PLCZ1,CAPZA3

chr8 140:140.2 COL22A1

chr20 22.4:22.6 FOXA2

chr8 98.4:98.6 TSPYL5

chr12 92.4:92.6 UBE2N,MRPL42,SOCS2,CRADD

chr6 29.2:29.4 OR2B3,OR5U1,OR5V1,OR12D3,LOC651503

chr7 148.4:148.6 ZNF783,PDIA4,ZNF786,ZNF425,ZNF398,ZNF212,ZNF282

chr12 87.2:87.4 KITLG

chr16 82.4:82.6 CDH13,HSBP1,EFCBP2,MBTPS1,OSGIN1,MLYCD,LOC146167

chr6 83.4:83.6chr22 24.2:24.4 ADRBK2

chr7 118.2:118.4chrX 121.2:121.4chr3 176.6:176.8 NAALADL2

chr11 87.2:87.4chr5 121:121.2 FTMT

chr13 59:59.2 DIAPH3

BiakaPygmy

BantuEurope

Mideast

S.AsiaE.Asia

Oceania

America

0.05

0.001

Figure 17: The top 1% of iHS signals in South Asia, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.

20

chr2 108.8:109 RANBP2,FLJ32745,EDAR

chr2 212.6:213 ERBB4

chr6 125.8:126.2 HEY2,NCOA7

chr2 108:108.4 SLC5A7,SULT1C3,SULT1C1,SULT1C2,GCC2

chr10 55.6:55.8 PCDH15

chr10 94.8:95.2 EXOC6,CYP26C1,CYP26A1,FER1L3,CEP55

chr5 112.2:112.6 APC,SRP19,DCP2,MCC,REEP5

chr10 55:55.2

chr11 25.2:25.6

chr12 1.2:1.4 ERC1

chr13 103.8:104

chr2 125.8:126.2

chr17 45.8:46.2 MRPL27,EME1,LRRC59,FLJ20920,CHAD,RSAD1,EPN3,SPATA20,CACNA1G,ABCC3,ANKRD40,CROP,XYLT2,MYCBPAP

chr4 170.2:170.6 CBR4,SH3RF1,NEK1

chr9 110.2:110.6

chr13 62.6:62.8

chr8 32:32.2 NRG1

chr22 38.2:38.4 MAP3K7IP1,MGAT3,SMCR7L,ATF4,RPS19BP1,CACNA1I

chr2 17:17.4

chr1 73.6:73.8

chr5 108:108.2 FER

chr5 25:25.2

chr10 52.8:53 PRKG1

chr10 94.4:94.6 KIF11,HHEX,EXOC6

chr20 58.2:58.4 LOC284757


chr16 17.2:17.4 XYLT1

chr7 86.2:86.4 GRM3,KIAA1324L

chr2 172.8:173.2 ITGA6,PDK1

chr16 64.2:64.4

chr2 38.2:38.4 CYP1B1,MGC34824,ARL6IP2

chr1 65.8:66 LEPR,PDE4B

chr4 105.2:105.6 CXXC4

chr15 62:62.2 DAPK2,FAM96A,SNX1,SNX22,PPIB,CSNK1G1

chr7 3.8:4.2 SDK1

chr10 11:11.2 CUGBP2

chr16 76:76.2 ADAMTS18

chr1 75.6:76 SLC44A5,ACADM,RABGGTB,MSH4

chr4 158.6:159


chr1 103.2:103.4 COL11A1

chr4 28.2:28.6

chr6 159:159.2 DYNLT1,VIL2,LOC202459,SYTL3

chr3 71.4:71.6 FOXP1

chr2 29.2:29.4 FLJ34931,CLIP4,ALK

chr10 4.2:4.4

chr22 34.8:35.2 APOL3,APOL4,APOL2,APOL1,MYH9,TXN2,FOXRED2,EIF3S7

chr4 144.4:144.6 USP38,GAB1

chr13 110.6:110.8 ARHGEF7,C13orf16

chrX 86.2:86.4

chr3 62.6:62.8 CADPS

chr10 15.4:15.6 C10orf38,ITGA8

chr7 126.6:127 GRM8,ZNF800,GCC1,ARF5,FSCN3,PAX4

chr3 176.6:177 NAALADL2

chr7 111.8:112 ZNF277P,IFRD1,FLJ39575

chr3 27.2:27.4 NEK10,SLC4A7

chr5 139:139.2 UBE2D2,CXXC5,PSD2,NRG2

chr7 50:50.2 ZPBP

chr11 81:81.2

chr3 169:169.2 SERPINI1,GOLPH4

chr9 15.8:16 C9orf93

chr4 160.4:160.8

chr1 232.8:233 IRF2BP2

chr1 74.6:74.8 TNNI3K,C1orf173

chr18 29.4:29.6

chr2 178.4:178.6 PDE11A

chr16 78.4:78.6

chr13 62:62.2

chr6 32.2:32.4 C6orf10,TNXB,CREBL1,FKBPL,PRRT1,PPT2,EGFL8,AGPAT1,RNF5,AGER,GPSM3,NOTCH4,LOC401252,PBX2

chr1 171.2:171.4 TNFSF18,TNFSF4

chr5 172.8:173 FAM44B

chr4 153:153.2

chr6 105.6:105.8 LIN28B,BVES,POPDC3,PREP

chr7 138.2:138.4 ZC3HAV1L,ZC3HAV1

chr3 197.4:197.6 TM4SF19,FLJ25996,ZDHHC19,OSTalpha,PCYT1A,MGC33212


chr9 23:23.2

chr10 73.6:73.8 ASCC1,C10orf104,DDIT4,DNAJB12,CBARA1

chr3 114.4:114.6 BOC,WDR52,CCDC52


chr5 38:38.2

chr2 56.6:56.8

BiakaPygmy

BantuEurope

Mideast

S.AsiaE.Asia

Oceania

America

0.05

0.001

Figure 18: The top 1% of iHS signals in East Asia, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.

21

chr16 11:11.4 PRM1,KIAA0350,SOCS1,TNP2,PRM3,PRM2,C16orf75,LOC400499

chr2 161.2:161.6chr6 47.6:47.8 GPR115,GPR111,CD2AP

chr10 110:110.2chr12 30.8:31 C1QDC1,TSPAN11

chr6 122.6:122.8 HSF2,SERINC1,PKIB

chr13 87.8:88.2chr5 141:141.2 HDAC3,C5orf16,FCHSD1,CENTD3,PCDH1,DIAPH1

chr4 68.6:68.8 TMPRSS11F,CHR415SYT,TMPRSS11B

chr8 33.4:33.6 FUT10,RBM13,C8orf41,RNF122,DUSP26

chr16 8.4:8.6 C16orf68

chr20 52:52.2 BCAS1,CYP24A1

chr3 158:158.2 FLJ16641

chr7 107.8:108 NRCAM,PNPLA8,THAP5,DNAJB9

chr1 159.8:160.2 FCGR2A,HSPA6,FCGR3A,FCGR2C,FCGR3B,FCGR2B,FCRLA,FCRLB,DUSP12,ATF6,OLFML2B

chr21 39.6:39.8 C21orf87,BRWD1,HMGN1,WRB,C21orf13,SH3BGR,LOC728776

chr6 123:123.2 PKIB,FABP7,SMPDL3A

chr7 100.4:100.6 MUC17,TRIM56,SERPINE1,AP1S1,VGF,FLJ39237,MOGAT3,PLOD3,ZNHIT1

chr6 73:73.2 RIMS1

chr8 95.6:95.8 RAD54B,KIAA1429,RBM35A,DPY19L4

chr3 21.2:21.4 ZNF659

chr6 54.6:55 FAM83B

chr12 30.2:30.4chr12 3.6:3.8 PRMT8,EFCAB4B,PARP11

chr3 24.8:25chr1 196.4:196.6 NEK7

chr5 80.8:81.2 SSBP2

chr21 40:40.2 B3GALT5,PCP4,LOC150084

chr5 153.6:153.8 GALNT10,SAP30L,HAND1

chr6 122.2:122.4chr11 69:69.2 CCND1,FLJ42258,ORAOV1,FGF19

chr2 3.2:3.4 TSSC1,TTC15

chr17 32.4:32.6 LHX1,AATF,ACACA

chr22 48.4:48.6 C22orf34,BRD1,ZBED4

chr2 54.8:55.2 SPTBN1,RTN4,FLJ42562

chr11 6.6:6.8 KIAA0409,ILK,TAF10,DCHS1,MRPL17,OR2AG2,OR2AG1,OR6A2,OR10A5,OR10A2,TPP1

chr12 73.6:73.8 KCNC2

chr7 131.6:131.8 PLXNA4B

chr2 17.8:18 SMC6,FLJ40869,KCNS3

chr6 119.2:119.4 MCMDC1,ASF1A,C6orf60

chr12 107.8:108 SSH1,DAO,SVOP,USP30,ALKBH2,UNG

chr2 36:36.2chr4 143.8:144

chr14 100:100.2 WDR25,KIAA1446,C14orf70

chr5 107.2:107.4 FBXL17

chr11 56.6:56.8 LRRC55,AGTRL1,TNKS1BP1

chr12 26.2:26.6 BHLHB3,SSPN,ITPR2

chr2 160.8:161 ITGB6,RBMS1

chr12 46.2:46.4 FLJ21908,P11,RAPGEF3

chr2 7:7.2 RNF144,RSAD2

chr6 154.4:154.6 OPRM1,PIP3−E

chr17 34.4:34.6 FBXO47,PLXDC1,CACNB1,RPL19,STAC2

chr18 32.6:32.8 FHOD3,C18orf10,KIAA1328

chr15 34:34.2chr10 31.2:31.4 ZNF438

chr17 36.2:36.4 KRT28,KRT40,KRT25,KRT26,KRT27,KRT10,KRT12,KRT20,KRT23,KRT39,KRTAP3−3,KRTAP3−2,KRTAP3−1,KRTAP1−5,KRTAP1−3,TMEM99

chr2 26.4:26.6 GPR113,SELI,C2orf39,OTOF,HADHB

chr2 52:52.2chr1 197.2:197.4chr5 164.6:164.8

chr5 154.8:155chr3 24.2:24.4 THRB

chrX 8.4:8.6 VCX−C,KAL1

chr2 169.4:169.6 NOSTRIN,SPBC25,G6PC2,ABCB11,DHRS9

chr6 47:47.2 GPR116,GPR110

chr15 56.2:56.4 AQP9

chr2 26.8:27 CENPA,KCNK3,DPYSL5,MAPRE3,C2orf18

chr4 60:60.2chr6 119.6:119.8 MAN1A1

chr1 89.6:89.8 GBP6,LRRC8B

chr4 164:164.2chr12 7.6:7.8 APOBEC1,GDF3,DPPA3,CLEC4C,NANOG

chr3 1.6:2chr7 122.6:122.8 SLC13A1

chr20 2.8:3 PTPRA,FAM113A,VPS16,GNRH2,MRPS26,OXT,AVP,UBOX5

chr16 78.6:78.8chr2 160.4:160.6 CD302,LY75,PLA2R1

chr15 50.8:51 KIAA1370,ONECUT1

chr6 35:35.2 C6orf107,TAF11,ANKS1A,TCP11

chr6 111.6:111.8 SLC16A10,KIAA1919,REV3L

chr13 37.4:37.6chr4 129.4:129.6 LARP2,PGRMC2

chr6 46.6:46.8 CYP39A1,TDRD6,PLA2G7,SLC25A27

chr15 56.8:57 ADAM10,SLTM,FAM63B

chr1 164.8:165

BiakaPygmy

BantuEurope

Mideast

S.AsiaE.Asia

Oceania

America

0.05

0.001

Figure 19: The top 1% of iHS signals in the Americas, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.

22

chr8 63.8:64 FAM77D

chr3 67.6:67.8 SUCLG2

chr2 165.2:165.6 GRB14,COBLL1,FLJ39822

chr2 126:126.2chr14 69.4:69.6 SMOC1,SLC8A3

chr5 61.2:61.4chr6 29.4:29.6 OR5U1,OR5V1,OR12D3,OR12D2,OR11A1,OR10C1,OR2H1,MAS1L

chr3 162.6:162.8 C3orf57,LOC131149

chr12 92.8:93 CRADD

chr2 165.8:166.2 SCN2A,SCN3A,FAM130A2

chr8 121.6:121.8 MTBP,SNTB1

chr9 1.6:1.8chr2 3.2:3.6 TSSC1,TTC15,ADI1,RNASEH1,RPS7,COLEC11

chr5 63.8:64 RGS7BP,P18SRP

chr20 5.8:6 C20orf196,CHGB,CGI−09,MCM8,CRLS1,C20orf75,C20orf42

chr1 183:183.2 EDEM3,FAM129A

chr2 22.6:22.8chr1 162.4:162.6

chr4 14.6:14.8 CPEB2

chr18 24.4:24.6chr15 96.8:97 FLJ39743,IGF1R

chr13 43.6:43.8 C13orf21

chr6 132.2:132.6 CTGF,ENPP1

chr15 51.6:51.8 WDR72

chr9 126.8:127 C9orf126,PPP6C,RABEPK,HSPA5

chr10 76.4:76.6 DUPD1,DUSP13,SAMD8,VDAC2,MYST4

chr13 110.4:110.6 ANKRD10,ARHGEF7

chr16 77.2:77.6 WWOX

chr1 70.2:70.4 LRRC40,SFRS11,LRRC7

chr3 162.2:162.4 PPM1L,B3GALNT1,NMD3

chr8 14:14.2 SGCZ

chr6 39.6:39.8 KIF6

chr13 46:46.2 LRCH1,ESD

chr8 63.2:63.6 FAM77D

chr4 113.4:113.6 C4orf16,TIFA,ALPK1

chr8 5.8:6chr7 120.4:120.8 ING3,FLJ21986,WNT16,FAM3C

chr6 160.2:160.4 IGF2R,PNLDC1,MAS1


chr17 61.2:61.4 CCDC46

chr14 68.4:68.6 ACTN1,WDR22

chr1 185.4:185.6chr17 40.2:40.4 ADAM11,DBF4B,HIGD1B,EFTUD2,CCDC103,GFAP,C1QL1,GJA7,LOC146909

chr2 212.8:213 ERBB4

chr10 80:80.2chr2 2.8:3

chr8 17.8:18 FGL1,PCM1,ASAH1

chr9 125:125.4 CRB2,STRBP,DENND1A

chr6 108.8:109 LACE1,FOXO3A

chr10 49.8:50 LRRC18,C10orf72

chr2 81.8:82chr3 38.4:38.6 XYLB,ENDOGL1,ACVR2B,SCN5A

chr2 212.4:212.6 ERBB4

chr5 64.4:64.6 SDCCAG10,ADAMTS6

chr3 26.6:26.8 LRRC3B

chr16 50.8:51 TNRC9

chr13 101.6:101.8 FGF14

chr1 182.4:182.6 C1orf21

chr1 207:207.2chr1 148.8:149 ECM1,ADAMTSL4,C1orf138,MCL1,ENSA,GOLPH3L,HORMAD1,CTSS,CTSK,ARNT

chr2 151.6:151.8 RBM43,NMI

chr4 60.6:60.8chr7 124.8:125

chr10 44.8:45 RASSF4,C10orf10,C10orf25,ZNF22

chrX 12.4:12.6 FRMPD4

chr9 0.6:1 ANKRD15,DMRT1,DMRT3,DMRT2

chr22 41:41.2 NFAM1,SERHL,CGI−96

chr5 114.8:115 FEM1C,TICAM2,TMED7

chr20 40:40.2 PTPRT

chr3 171.4:171.6 PHC3,PRKCI,SKIL,CLDN11

chr2 198.2:198.4 RFTN2,MARS2,BOLL

chr7 103.6:103.8 LHFPL3,ORC5L

chr7 19.2:19.4 FERD3L

chr11 33.6:33.8 C11orf69,CD59,FBXO3,LMO2

chr5 169.6:169.8 LCP2,KCNIP1,KCNMB1

chr1 175.4:175.6 ASTN1,FAM5B

chr22 41.6:41.8 ARFGAP3,PACSIN2,TTLL1,BIK

chr2 213.6:213.8 IKZF2

chr10 43.4:43.6 ZNF239,ZNF485,ZNF32

chr6 56.2:56.4 COL21A1,DST

chr12 41.8:42 ADAMTS20

chr12 119.4:119.6 COQ5,COX6A1,TRIAP1,15E1.2,SFRS9,DYNLL1,RNF10,POP5,CABP1,KIAA0152,ACADS,MGC5139

chr18 9.2:9.4 ANKRD12,TWSG1

chr20 17.2:17.4 PCSK2,BFSP1

chr10 76:76.2 ADK

chr5 58.4:58.6 PDE4D

chr7 23.8:24 STK31

BiakaPygmy

BantuEurope

Mideast

S.AsiaE.Asia

Oceania

America

0.05

0.001

Figure 20: The top 1% of iHS signals in Oceania, ordered from top to bottom in order of significance.See the caption of Figure 1 in the main text for details.

23

chr13 24.2:24.4 ATP12A,CENPJ,RNF17

chr20 34.8:35 NDRG3,DSN1,C20orf117,C20orf118,SAMHD1

chr17 0.6:0.8 VPS53,FAM57A,C17orf25,RNMTL1,NXN,TIMM22,GEMIN4

chr6 164.6:164.8chr19 47:47.2 CEACAM6,LYPD4,RPS19,ARHGEF1,RABAC1,ATP1A3,GRIK5,DMRTC2,CEACAM3,CD79A

chr6 52:52.2 PKHD1,IL17A,IL17F,MCM3

chr3 121.8:122 NDUFB4,GTF2E1,HGD,RABL3

chr14 84.6:84.8chr11 18.6:18.8 SPTY2D1,TMEM86A,IGSF22,PTPN5,UEVLD

chr17 21.2:21.6 MAP2K3,KCNJ12

chr11 63:63.2 HRASLS5,LGALS12,RARRES3,HRASLS2,HRASLS3,DKFZP564J0863,RTN3

chr13 59.6:59.8 DIAPH3

chr1 207:207.2chr2 59:59.2

chr3 194.2:194.4 HRASLS

chr19 45.6:45.8 PLD3,HIPK4,SERTAD1,SERTAD3,BLVRB,SHKBP1,PRX,SPTBN4,LTBP4

chr12 106.2:106.4 BTBD11

chr18 44.8:45 DYM

chr17 58.8:59 CYB561,ACE,KCNH6,CCDC44,WDR68

chr10 92:92.2chr13 58.6:58.8

chr10 86:86.2 LRRC21,LRRC22,PCDH21,RGR,KIAA1128

chr10 42.8:43 RASGEF1A,RET,GALNACT−2

chr3 148.4:148.6 ZIC4,ZIC1

chr22 34:34.2 HMG2L1,TOM1,HMOX1,MCM5

chr10 12.4:12.6 CAMK1D

chr1 115.6:115.8 NGFB

chr21 43.6:43.8 SNF1LK,FLJ41733,C21orf125,HSF2BP

chr12 54.6:54.8 IKZF4,WIBG,DGKA,SILV,CDK2,RAB5B,SUOX,RPS26,ERBB3,RPL41,ZC3H10,FAM62A,MYL6B,MYL6,SMARCC2,PA2G4

chr6 72.4:72.6chr6 158.6:158.8 TULP4

chr2 105.2:105.4 GPR45,TGFBRAP1,C2orf49,FHL2

chr7 96.4:96.6 DLX6,DLX5,ACN9

chr3 185.4:185.6 DVL3,AP2M1,ABCF3,ALG3,MGC2408,ECE2,CAMK2N2,PSMD2,EIF4G1,C3orf40,CLCN2,POLR2H,THPO,CHRD

chr14 90:90.2 TTC7B

chr7 153.4:153.6 DPP6

chr16 86.4:86.6 KLHDC4,SLC7A5,CA5A,BANP

chrX 41.4:41.8 CASK,GPR34,GPR82

chrX 33.2:33.4 DMD

chr7 38.8:39 VPS41,POU6F2

chr20 16.4:16.6 C20orf23

chr8 106.4:106.6 ZFPM2

chr7 45.2:45.4 RAMP3

chr17 52.4:52.6 AKAP1,COIL,SCPEP1

chr11 43.4:43.6 TTC17

chr17 76:76.2 KIAA1303,RNF213,FLJ35220,NPTX1

chr8 4.8:5 CSMD1

chr19 48.4:48.6 PSG5,PSG4,PSG9,TEX101,CD177

chr5 60.8:61 FLJ37543

chr1 113.8:114.2 MAGI3,PHTF1,RSBN1,PTPN22,C1orf178,AP4B1,DCLRE1B

chr7 36.4:36.6 KIAA0895,ANLN,AOAH

chr1 39.2:39.4 RHBDL2,C1orf108,NDUFS5,MACF1

chr2 49.8:50 NRXN1

chr12 28:28.2 PTHLH

chr7 106.4:106.8 PRKAR2B,HBP1,COG5

chr1 177.2:177.4 RALGPS2,FAM20B,ABL2,TOR3A

chr8 26.6:26.8 ADRA1A,DPYSL2

chr2 50.8:51 NRXN1

chr8 59.6:59.8 CYP7A1,SDCBP,NSMAF

chr3 45.6:45.8 LARS2,SACM1L,SLC6A20,LZTFL1,LIMD1

chr16 4.2:4.4 TFAP4,Magmas,CORO7,VASN,DNAJA3,GLIS2

chr9 134.8:135 C9orf9,TSC1,GFI1B,GTF3C5,CEL,RALGDS,GBGT1

chr17 3.4:3.6 TRPV1,CTNS,TRPV3,CARKL,TAX1BP3,TMEM93,P2RX5,ITGAE,GSG2

chr11 13.6:13.8 MLSTD2

chr19 0.6:0.8 HCN2,POLRMT,FGF22,FLJ45684,RNF126,PRSSL1,C19orf21,PTBP1,PRG2,AZU1,PRTN3,ELA2,CFD,THRAP5,C19orf22,FSTL3,PALM

chr1 82.4:82.8chr12 97.6:97.8 IKIP,APAF1,ANKS1B

chr19 5.2:5.4 PTPRS,ZNRF4

chr11 132.4:132.6 OPCML

chr10 15.8:16.2 ITGA8,C10orf97

chr7 62.2:62.4chr18 40.8:41 SETBP1


chr19 50.4:50.6 TRAPPC6A,EXOC3L2,MARK4,CKM,ERCC2,PPP1R13L,CD3EAP,ERCC1,BLOC1S3,KLC3

chr11 76.4:76.6 PHCA,CAPN5,OMP,GDPD4,B3GNT6,MYO7A

chr9 25:25.2chr14 100.2:100.4 C14orf70,DLK1

chr7 23:23.2 FAM126A,KLHL7,NUPL2

chr4 109.2:109.4 LEF1,HADH

chrX 62.8:63 ARHGEF9

chr20 37.8:38chrX 8:8.2 VCX2

chr4 180.4:180.6chr4 147:147.2 LOC152485

chr2 213.6:213.8 IKZF2

chr22 26.4:26.6 MN1,PITPNB

chr10 104:104.2 NFKB2,ELOVL3,PITX3,GBF1,PSD,FBXL15,CUEDC2,C10orf95,TMEM180,ACTR1A

chr1 159.6:159.8 SDHC,C1orf192,FCGR2A,HSPA6,FCGR3A,FCGR2C

chr1 11.6:11.8 FBXO2,FBXO44,FBXO6,MAD2L2,C1orf187,MTHFR,CLCN6,NPPA,NPPB,AGTRAP

chr6 151:151.2 PLEKHG1,MTHFD1L

chr10 91:91.2 LIPA,IFIT2,IFIT3,IFIT1L,IFIT5,SLC16A12,IFIT1,CH25H

chr6 144.2:144.4 PHACTR2,LTV1,PLAGL1

chr14 100.8:101chr7 44.2:44.6 GCK,YKT6,CAMK2B,NPC1L1,DDX56,TMED4,OGDH,NUDCD3

chr17 68.8:69 C17orf80,CDC42EP4,SDK2

chr3 156.2:156.4 MME,FLJ46120

chr11 29.8:30 KCNA4

chr11 11.4:11.6 GALNTL4

chr7 0.8:1 HEATR2,C7orf20,CENTA1,CYP2W1,MGC11257,FLJ44124,UNC84A,COX19

chr11 115.8:116chr11 121.6:121.8

chr18 62.4:62.6 CDH19

chr14 74.8:75 FOS,JDP2

chr21 34:34.2 ITSN1,ATP5O

chr10 9.6:9.8chr6 165.4:165.6 C6orf118

chr14 73.2:73.4 ACOT6,DNAL1,PNMA1,C14orf43,ZADH1,ZNF410

chr5 91.8:92chr12 16.6:16.8 LMO3

chr7 17.6:17.8 SNX13

chr9 138.4:138.6 SNAPC4,GPSM1,CARD9,SDCCAG3,PMPCA,INPP5E,C9orf163,NOTCH1,LOC728489,KIAA0310

chr22 20.2:20.4 LOC220686,LOC375133,UBE2L3,LOC150223,CCDC116,SDF2L1,PPIL2,YPEL1,MAPK1

chr11 61.2:61.4 C11orf11,C11orf9,C11orf10,FEN1,FADS1,FADS2,FADS3,RAB3IL1

chr9 99.6:99.8 ANP32B,C9orf156,FOXE1,HEMGN

chr17 42.6:42.8 CDC27,MYL4,ITGB3,C17orf57

chr9 27.4:27.6 IFNK,MOBKL2B,C9orf72

chr11 34.2:34.4 ABTB2,CAT

chr1 41.2:41.4 CTPS,SLFNL1,SCMH1

chr11 107.2:107.4 SLC35F2,RAB39,CUL5

chr7 43.4:43.6 C7orf44,HECW1,STK17A

chr2 44:44.2 ABCG8,LRPPRC,PPM1B

chr15 82.6:82.8 KIAA1920

chr8 135.2:135.4

BiakaPygmy

BantuEurope

Mideast

S.AsiaE.Asia

Oceania

America

0.05

0.001

Figure 21: The top 1% of XP-EHH signals in the Bantu, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.

24

chr6 164.6:164.8chr10 9.6:9.8chr17 0.6:0.8 VPS53,FAM57A,C17orf25,RNMTL1,NXN,TIMM22,GEMIN4

chr6 52:52.2 PKHD1,IL17A,IL17F,MCM3

chr8 106.4:106.6 ZFPM2

chr11 18.6:18.8 SPTY2D1,TMEM86A,IGSF22,PTPN5,UEVLD

chr16 86.4:86.6 KLHDC4,SLC7A5,CA5A,BANP

chr7 106.2:106.4 PIK3CG

chr10 0.6:0.8 DIP2C,C10orf108,LARP5

chr19 52:52.4 SLC1A5,AP2S1,GRLF1,NPAS1,TMEM160,SAE1,BBC3,FKRP

chr1 82.4:82.6chr13 59.6:59.8 DIAPH3

chr11 34.2:34.4 ABTB2,CAT

chr13 107.6:107.8 LIG4,ABHD13,TNFSF13B

chr3 115.4:115.6 DRD3,ZNF80,VSIG9,ZBTB20

chr11 29.8:30 KCNA4

chr9 115:115.2 RGS3,SLC31A2,SLC31A1,CDC26,PRPF4,RNF183,WDR31,BSPRY,HDHD3,ALAD,POLE3,C9orf43

chr18 52:52.2 FLJ45743

chr22 38.4:38.6 CACNA1I,ENTHD1,GRAP2

chr18 44.8:45 DYM

chr14 100.2:100.4 C14orf70,DLK1

chr9 25:25.2chr1 198.6:198.8 ZNF281,KIF14

chr20 60.6:60.8 FLJ30313,C20orf166,SLCO4A1,NTSR1

chr8 126.8:127chr3 2.4:2.6 CNTN4

chr5 178.2:178.4 GRM6,ZNF354B,ZFP2,ZNF454,ZNF354C

chr11 32.4:32.6 WT1,WIT1,PCID1,CCDC73

chr15 49.4:49.6 GLDN,CYP19A1,DMXL2

chr16 27.6:27.8 KIAA0556,GSG1L

chr17 58.8:59 CYB561,ACE,KCNH6,CCDC44,WDR68

chr8 0.2:0.4 C8orf42,ZNF596,FBXO25

chr4 4.6:4.8 STX18

chr19 48.4:48.6 PSG5,PSG4,PSG9,TEX101,CD177

chr8 125.4:125.6 TMEM65,TRMT12,RNF139,TATDN1,NDUFB9,MTSS1

chr6 20:20.2 MBOAT1

chr7 139.2:139.4 TBXAS1,PARP12,KIAA1718

chr11 63:63.2 HRASLS5,LGALS12,RARRES3,HRASLS2,HRASLS3,DKFZP564J0863,RTN3

chrX 91.6:91.8 PCDH11X

chrX 115:115.2 AGTR2

chr14 94.6:94.8 DICER1,FLJ45244,CLMN

chr19 56.8:57 ZNF175,SIGLEC5,HAS1,FPR1,FPRL1,FPRL2

chr22 15.4:15.6 CESK1,XKR3

chr9 134.8:135 C9orf9,TSC1,GFI1B,GTF3C5,CEL,RALGDS,GBGT1

chr5 177.4:177.6 LOC653316,PROP1,N4BP3,RMND5B,NOLA2,HNRPAB,AGXT2L2,COL23A1,LOC653314

chr17 76.6:76.8 KIAA1303,AZI1,CHMP6,BAIAP2,FLJ44861,C17orf56,MGC15523,AATK

chr6 67.2:67.4chr15 23.4:23.6 ATP10A

chr10 104:104.2 NFKB2,ELOVL3,PITX3,GBF1,PSD,FBXL15,CUEDC2,C10orf95,TMEM180,ACTR1A

chr11 94.8:95chr11 13.6:13.8 MLSTD2

chr11 61.2:61.4 C11orf11,C11orf9,C11orf10,FEN1,FADS1,FADS2,FADS3,RAB3IL1

chr3 195.4:195.6 GP5,LRRC15,CPN2

chr9 132.8:133 LAMC3,ABL1,P518,FIBCD1,C9orf58,NUP214

chr13 106.6:106.8 LOC728215

chr3 121.8:122 NDUFB4,GTF2E1,HGD,RABL3

chr13 89.8:90chr10 12.4:12.6 CAMK1D

chr19 45.6:45.8 PLD3,HIPK4,SERTAD1,SERTAD3,BLVRB,SHKBP1,PRX,SPTBN4,LTBP4

chr12 66.2:66.4 DYRK2

chr3 156.2:156.4 MME,FLJ46120

chr17 21.2:21.6 MAP2K3,KCNJ12

chr7 153:153.2 DPP6,FLJ16734

chr2 11.8:12 LPIN1

chr1 238:238.2 CHRM3

chr22 34:34.2 HMG2L1,TOM1,HMOX1,MCM5

chr1 1.8:2.2 GNB1,CALML6,TMEM52,LOC339457,GABRD,PRKCZ,SKI,MORN1,C1orf86,KIAA1751

chr9 112.8:113 EDG2

chr2 183.4:183.6 DNAJC10,FRZB,NCKAP1

chr13 58.6:58.8chr16 64:64.2

chr20 16.4:16.6 C20orf23

chr3 98.8:99 ARL6,EPHA6

chr1 57:57.2 C1orf168,C8A,C8B,DAB1

chr16 31.2:31.6 ITGAM,ITGAX,ITGAD,COX6A2,ARMC5,TGFB1I1,SLC5A2,C16orf58,ERAF


chr11 0.6:0.8 CEND1,C11orf35,RASSF7,KIAA1542,SCT,DRD4,DEAF1,EPS8L2,TALDO1,SLC25A22,LRDD,RPLP2,PNPLA2,EFCAB4A,CD151,POLR2L,TSPAN4,IRF7,MUCDHL,TMEM80,PDDC1

chr8 59.2:59.4 C8orf72

chr6 24:24.2 NRSN1

chr17 27.8:28 PSMD11,CDK5R1,MYO1D

chr7 106.6:106.8 PRKAR2B,HBP1,COG5

chr14 43.6:43.8chrX 41.6:41.8 CASK

chr1 171.2:171.4 TNFSF18,TNFSF4

chr2 105.2:105.4 GPR45,TGFBRAP1,C2orf49,FHL2

chrX 102.8:103 TCEAL3,TCEAL1,MORF4L2,TMEM31,PLP1,RAB9B

chr15 76.4:76.6 DNAJA4,WDR61,CRABP1,IREB2,LOC123688,PSMA4,CHRNA5

chr17 9:9.2 NTN1,STX8

chr1 12.2:12.4 TNFRSF1B,VPS13D

chr4 13:13.2 RAB28,BAPX1,FAM44A

chr12 29.8:30 TMTC1

chr5 56.8:57 DKFZp686D0972

chr20 34.8:35 NDRG3,DSN1,C20orf117,C20orf118,SAMHD1

chr11 133.2:133.4 SPATA19,JAM3

chr19 1:1.2 GRIN3B,C19orf6,CNN2,ABCA7,HMHA1,POLR2E,SBNO2,STK11,C19orf26,ATP5D,MIDN,C19orf23,CIRBP,C19orf24,EFNA2,GPX4

chr11 113.8:114 FAM55D,C11orf71,RBM7,REXO2,FAM55A

chr2 171:171.2 MYO3B

chr18 40.8:41 SETBP1

chr10 12:12.2 C10orf47,UPF2,DHTKD1,SEC61A2,NUDT5

chr6 148.8:149 SASH1

chr16 55.4:55.6 NLRC5,NUP93,SLC12A3,HERPUD1,CETP

chr19 5.4:5.6 ZNRF4,PLAC2,SAFB,P117,HSD11B1L,RPL36,LONP1,SAFB2

chr8 109.6:109.8 TTC35

chr15 20.4:20.6 TUBGCP5,CYFIP1,NIPA2,NIPA1

chr17 64.8:65 ABCA10,ABCA5,MAP2K6

chr7 5.2:5.4 WIPI2,FBXL18,SLC29A4,KIAA1856

chr4 114.4:114.6 ANK2,CAMK2D

chr19 38:38.2 SLC7A9,CCDC123,C19orf40,RHPN2

chr12 55.8:56 KIAA0286,STAT6,LRP1,NXPH4,SHMT2,NDUFA4L2,STAC3,R3HDM2,NAB2

chr1 158.4:158.6 ATP1A2,ATP1A4,CASQ1,PEA15,WDR42A,PEX19,COPA,NCSTN,NHLH1,VANGL2

chr3 9.2:9.4 SRGAP3,THUMPD3,SETD5

chr5 126.2:126.4 LMNB1,MARCH3

chr12 29:29.2chr2 111.8:112chr6 155:155.2 RBM16

chr18 5.2:5.4 ZFP161,EPB41L3

chr9 83.4:83.6 TLE1

chr12 102.6:102.8 STAB2,NT5DC3,HSP90B1

chr1 39.2:39.4 RHBDL2,C1orf108,NDUFS5,MACF1

chr3 12.8:13 TMEM40,RPL32,IQSEC1,CAND2

chr11 43.4:43.6 TTC17

chr7 155.4:155.6chr19 0.4:0.6 MADCAM1,C19orf19,CDC34,GZMM,BSG,HCN2,POLRMT,FGF22,FLJ45684,RNF126,PRSSL1,C19orf20,FSTL3

chr21 43.2:43.4 WDR4,NDUFV3,PKNOX1,CBS,U2AF1

chr16 53.2:53.4

BiakaPygmy

BantuEurope

Mideast

S.AsiaE.Asia

Oceania

America

0.05

0.001

Figure 22: The top 1% of XP-EHH signals in the Biaka Pygmies, ordered from top to bottom inorder of significance. See the caption of Figure 1 in the main text for details.

25

chr21 16.8:17 C21orf34


chr17 60.6:61 RGS9,AXIN2

chr9 90:90.4 SPIN1,C9orf121

chr3 131.4:131.8 FLJ35880

chr12 87.4:87.8 KITLG

chr8 140:140.2 COL22A1

chr10 65.4:65.8chr17 56.2:56.6 BCAS3

chr7 119.6:120 KCND2

chr18 11.2:11.4chr14 61:61.2 PRKCH,HIF1A

chr10 83.6:83.8 NRG3

chr4 82:82.4 C4orf22,BMP3,PRKG2

chr1 35.4:35.8 SFPQ,ZMYM4,KIAA0319L,NCDN,TFAP2E,PSMB2,ZMYM1


chr15 67.4:67.8 GLCE,PAQR5,KIF23,RPLP1,LOC729416

chr18 19.6:20 LAMA3,CABYR,OSBPL1A,C18orf17

chr6 0:0.2 DUSP22,FLJ43763

chr4 32.6:33chr5 109.6:110

chr5 21.8:22 CDH12

chr7 18.6:18.8 HDAC9

chr3 72.6:72.8 RYBP

chr5 26.4:26.8chr3 25.8:26 NGLY1,OXSM

chr4 55.8:56 SRD5A2L,TMEM165,CLOCK

chr3 176.6:176.8 NAALADL2

chr5 74.4:74.8 GCNT4,HMGCR,COL4A3BP,POLK

chr3 31.2:31.6 STT3B

chr9 3.2:3.4 RFX3

chr12 2.6:2.8 FKBP4,ITFG2,NRIP2,FOXM1,CACNA1C

chrX 110:110.4 PAK3,CAPN6,DCX

chr4 172.6:172.8chr20 58.2:58.4 LOC284757

chr4 5.2:5.4 STK32B



chr22 20.6:20.8 MAPK1,PPM1F,TOP3B

chr15 89.8:90chr10 84:84.2 NRG3

chr18 7.4:7.8 PTPRM

chr20 52.4:52.6 DOK5


chr1 244:244.2 SMYD3

chr1 36:36.4 FLJ38984,CLSPN,EIF2C4,EIF2C1,EIF2C3,TEKT2,ADPRHL2,COL8A2,TRAPPC3,MAP7D1


chr4 60.8:61.2chr17 55.6:56 CA4,USP32,C17orf64,APPBP2,PPM1D

chr5 75:75.4 C5orf37,SV2C

chr2 152.2:152.4 NEB,ARL5A,CACNB4

chr6 14.8:15chr12 57.6:57.8 LRIG3

chr8 16.2:16.4chr11 64:64.2 SLC22A11,SLC22A12,NRXN2

chr3 3.8:4 LRRN1


chr6 143:143.2 HIVEP2

chr10 22.4:22.8 COMMD3,BMI1,SPAG6

chr11 41.8:42chr21 29.8:30.2 GRIK1

chr3 192:192.2chr7 33.6:33.8 BBS9

chr10 118:118.4 GFRA1,C10orf96,PNLIPRP3,PNLIP,PNLIPRP1,C10orf82,PNLIPRP2,HSPA12A

chrX 36:36.2 CXorf59

chr17 51.4:51.6 ANKFN1

chr15 46.6:46.8 CEP152,FBN1

chr7 37:37.2 ELMO1

chr16 64.6:64.8chr5 90.4:90.6 GPR98

chr3 100.4:100.8 COL8A1

chr2 167.6:168 CMYA3

chr4 14.2:14.4chr8 18.6:18.8 PSD3

chr4 33.2:33.6chr15 27:27.4 APBA2,NDNL2

chr4 29.4:29.8chr6 108:108.2 SCML4,FLJ10159

chr13 73.6:73.8 KLF12

chr19 7.2:7.6 ARHGEF18,PEX11G,C19orf45,ZNF358,MCOLN1,XAB2,PCP2,STXBP2,RETN,PNPLA6,C19orf59,INSR,KIAA1543

chr1 228:228.2chr1 192.4:192.6chr6 105.6:105.8 LIN28B,BVES,POPDC3,PREP

chr1 160.2:160.4 ATF6,OLFML2B,NOS1AP

chr18 64.8:65 CCDC102B

chr6 75.6:75.8chr6 124:124.2 TCBA1,TRDN

chr15 57.2:57.4 RNF111,CCNB2,MYO1E,LDHAL6B

chr2 120.8:121 RALB,INHBB

chr2 222.2:222.4chrX 98.4:98.6chr1 234.8:235 LGALS8,HEATR1,ACTN2,MTR

BiakaPygmy

BantuEurope

Mideast

S.AsiaE.Asia

Oceania

America

0.05

0.001

Figure 23: The top 1% of XP-EHH signals in Europe, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.

26

chr21 16.8:17 C21orf34


chr8 140:140.2 COL22A1


chr6 0:0.2 DUSP22,FLJ43763

chr14 62.6:63 KCNH5,RHOJ,GPHB5,PPP2R5E

chr17 56:56.4 APPBP2,PPM1D,BCAS3

chr5 26.4:26.8chr14 61:61.2 PRKCH,HIF1A

chr8 139.6:139.8 C8ORFK32,COL22A1

chr12 87.2:87.6 KITLG

chr3 25.6:26 RARB,TOP2B,NGLY1,OXSM

chr7 119.4:119.8 KCND2

chr11 8:8.2 EIF3S5,TUB,RIC3,LMO1

chr10 65.4:65.8chr15 46.6:46.8 CEP152,FBN1

chr5 109.6:110chr2 238:238.2 COL6A3,PRLH,RAB17,MLPH

chr3 31.2:31.6 STT3B

chr18 55.8:56chr6 108:108.2 SCML4,FLJ10159

chr15 27:27.4 APBA2,NDNL2

chr5 23.2:23.6 PRDM9

chr20 52.4:52.6 DOK5

chr6 123.8:124.2 TCBA1,TRDN

chr17 52.6:53 AKAP1,MSI2

chr10 22.2:22.6 COMMD3,DNAJC1

chr9 1.8:2 SMARCA2

chr19 7.2:7.6 ARHGEF18,PEX11G,C19orf45,ZNF358,MCOLN1,XAB2,PCP2,STXBP2,RETN,PNPLA6,C19orf59,INSR,KIAA1543


chrX 35.8:36.2 CXorf59,CXorf22

chr10 118:118.4 GFRA1,C10orf96,PNLIPRP3,PNLIP,PNLIPRP1,C10orf82,PNLIPRP2,HSPA12A

chr8 17.6:17.8 MTUS1,FGL1,PCM1

chr21 29.8:30.2 GRIK1

chr3 131.6:131.8 FLJ35880

chr1 35.2:35.6 SFPQ,ZMYM4,ZMYM1,ZMYM6

chr1 35.8:36.2 KIAA0319L,NCDN,TFAP2E,PSMB2,FLJ38984,CLSPN,EIF2C4,EIF2C1,EIF2C3

chr16 77:77.2 WWOX

chr7 33.6:33.8 BBS9

chr12 57.6:57.8 LRIG3

chr3 26.2:26.4chr15 67.6:67.8

chr12 124.6:124.8 TMEM132B

chr11 64:64.4 SLC22A11,SLC22A12,NRXN2,RASGRP2,PYGM,SF1,MAP4K2,MEN1,CDC42BPG,EHD1,KIAA0404,PPP2R5B

chr1 65:65.2 RAVER2,JAK1

chr9 32.6:32.8 NDUFB6,TAF1L,LOC401498

chr1 192.2:192.6chr3 112.6:112.8 CD96,ZBED2

chr6 14.8:15chr18 19.8:20 LAMA3,CABYR,OSBPL1A,C18orf17


chr10 25.8:26 GPR158

chr3 113:113.2 TMPRSS7,PLCXD2,PHLDB2,ABHD10,TAGLN3

chr3 100.4:100.8 COL8A1

chr10 22.8:23 PIP5K2A

chr5 21.8:22 CDH12


chr18 7.4:7.6 PTPRM

chr4 172.6:172.8chr9 90.2:90.4 SPIN1,C9orf121

chr2 222.2:222.4chr17 60.6:60.8 RGS9

chr20 21.8:22chr16 1.8:2 RNF151,MAPK8IP3,NME3,MRPS34,EME2,SPSB3,NUBP2,IGFALS,FAHD1,C16orf73,SEPX1,RPL3L,NDUFB10,RPS2,TBL3,NOXO1,GFER,SYNGR3,ZNF598,SLC9A3R2,NTHL1,HAGH,TSC2,LOC91561,HS3ST6

chr13 103:103.2chr9 107:107.2 SLC44A1

chr2 213:213.2 ERBB4

chr10 83.6:84 NRG3

chr3 111.2:111.4chr13 33.4:33.6 RFC3

chr4 60.8:61chr5 19.6:19.8 CDH18

chr20 15.6:15.8 C20orf133

chr1 246:246.2 OR5AT1,OR11L1,OR2W3,OR2T8,OR2L13,OR2L8,OR2AK2,TRIM58,OR1C1,OR5AY1

chr1 244:244.2 SMYD3


chr12 87.8:88chr17 51.4:51.6 ANKFN1

chr4 170.4:170.6 SH3RF1,NEK1


chr3 176.6:176.8 NAALADL2

chr8 116:116.2chr11 103.8:104chr6 128.8:129 PTPRK

chr6 4.6:4.8 KU−MEL−3,CDYL

chr9 16:16.2 C9orf93

chr5 11.6:11.8 CTNND2

chr12 125.6:125.8chr2 152.2:152.4 NEB,ARL5A,CACNB4

chr11 87:87.2chr5 24.6:24.8 CDH10

chr4 33.4:33.6chr4 14.2:14.4

BiakaPygmy

BantuEurope

Mideast

S.AsiaE.Asia

Oceania

America

0.05

0.001

Figure 24: The top 1% of XP-EHH signals in the Middle East, ordered from top to bottom in orderof significance. See the caption of Figure 1 in the main text for details.

27


chr7 119.4:119.8 KCND2


chr21 16.8:17 C21orf34


chr17 60.6:60.8 RGS9

chr4 29.4:29.8chr17 56.2:56.6 BCAS3

chr12 87.4:87.8 KITLG


chr16 84.4:84.6 COX4NB,COX4I1,IRF8

chr17 50.8:51.2 HLF,MMD,TMEM100,PCTP

chr20 52.4:52.6 DOK5


chr10 65.4:65.8chr15 46.6:46.8 CEP152,FBN1

chr12 2.6:2.8 FKBP4,ITFG2,NRIP2,FOXM1,CACNA1C

chr6 0:0.2 DUSP22,FLJ43763

chr4 41.8:42 SLC30A9,CCDC4

chr10 84:84.2 NRG3

chr17 52:52.2 NOG


chr10 22.4:22.8 COMMD3,BMI1,SPAG6

chr10 59.2:59.4chr14 62.6:63 KCNH5,RHOJ,GPHB5,PPP2R5E

chr10 100.2:100.4 C10orf33,HPS1,HPSE2

chr12 57.6:57.8 LRIG3

chr7 118.2:118.6chr2 178:178.4 PDE11A,AGPS,TTC30A,TTC30B



chr8 139.6:140 C8ORFK32,COL22A1

chr3 26.2:26.4chr12 125.6:125.8

chr3 31.2:31.6 STT3B

chr9 90.2:90.4 SPIN1,C9orf121

chr4 82.2:82.4 BMP3,PRKG2

chr22 20.6:20.8 MAPK1,PPM1F,TOP3B

chr15 27:27.4 APBA2,NDNL2

chr10 83.6:83.8 NRG3


chr21 16.2:16.6 USP25,C21orf34

chr7 18.6:18.8 HDAC9

chr4 5.2:5.4 STK32B

chr11 109.2:109.4chr7 118.8:119.2

chr5 109.6:110chr9 3.2:3.4 RFX3

chr11 87:87.4chr21 15.8:16 USP25

chr2 218.8:219 GPBAR1,PNKD,ARPC2,TMBIM1,MGC50811,SLC11A1,CTDSP1,VIL1,USP37,AAMP

chr7 145.4:145.8 CNTNAP2

chr6 143:143.2 HIVEP2

chr17 55.6:56 CA4,USP32,C17orf64,APPBP2,PPM1D

chr4 84.2:84.4 LIN54,COPS4,PLAC8,HPSE,COQ2

chr12 126.8:127chr1 35.6:35.8 ZMYM4,KIAA0319L,NCDN,TFAP2E,PSMB2


chr2 237.6:237.8 COPS8

chr12 65.6:66 CAND1

chr5 26.4:26.6chr15 67.6:67.8chrX 111:111.2 ZCCHC16,TRPC5


chr13 91.2:91.6 GPC5

chr8 37:37.2chr18 64.8:65 CCDC102B

chr15 33.6:33.8 ATPBD4

chr17 52.6:52.8 AKAP1,MSI2

chr11 129.4:129.6 PRDM10,C11orf37,APLP2,ST14,ZBTB44

chr9 107:107.2 SLC44A1

chr2 205.8:206 PARD3B

chr1 203:203.2 NFASC

chr1 36.2:36.4 EIF2C1,EIF2C3,TEKT2,ADPRHL2,COL8A2,TRAPPC3,MAP7D1

chr12 116.4:116.6 KSR2

chr2 231.4:231.6 GPR55,CAB39,ITM2C,PSMD1

chr3 142.2:142.6 SLC25A36,SPSB4,ACPL2,ZBTB38

chr17 11:11.2 FLJ45455

chr3 167:167.2 BCHE

chr10 118:118.2 GFRA1,C10orf96,PNLIPRP3

chr21 29.8:30 GRIK1

chr13 32.2:32.4 APRIN

chr4 33.4:33.6chr1 187.4:187.6chr13 103:103.2

chr3 43.2:43.4 TMEM16K,SNRK

chr10 59.6:59.8 IPMK,ZCD1,UBE2D1,TFAM

chr17 51.4:51.6 ANKFN1

chrX 110.6:110.8 ALG13

chr18 11.2:11.4chr2 192:192.2 MYO1B

BiakaPygmy

BantuEurope

Mideast

S.AsiaE.Asia

Oceania

America

0.05

0.001

Figure 25: The top 1% of XP-EHH signals in South Asia, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.

28

chr11 25.2:25.6

chr15 61.4:61.8 APH1B,CA12,USP3,FBXL22,HERC1

chr2 177:177.4

chr22 21.6:21.8 RTDR1,GNAZ,RAB36

chr4 158.6:159


chr17 56.2:56.6 BCAS3

chr4 5.8:6.2 EVC2,CRMP1,FLJ46481,JAKMIP1,EVC

chr8 139:139.2 C8ORFK32

chr2 9.2:9.6 ITGB1BP1,DDEF2,CPSF3,IAH1,ADAM17,YWHAQ

chr3 26.2:26.4


chr21 16.2:16.6 USP25,C21orf34

chr2 125.4:125.8 CNTNAP5

chr2 198.6:199 PLCL1

chr2 17.8:18 SMC6,FLJ40869,KCNS3

chr2 108.8:109 RANBP2,FLJ32745,EDAR

chr16 64.2:64.6

chr4 159.2:159.4 C4orf18,TMEM144

chr20 58.2:58.4 LOC284757

chr2 17.2:17.6 VSNL1

chr10 59.2:59.4

chr8 10.8:11.2 C8orf15,MTMR9,AMAC1L2,XKR6


chr1 103.2:103.6 COL11A1


chr6 105.6:106 LIN28B,BVES,POPDC3,PREP

chr21 41.4:41.6 PLAC4,BACE2,FAM3B

chr10 94.4:94.8 KIF11,HHEX,EXOC6,CYP26C1,CYP26A1

chr17 53.2:53.6 OR4D2,MRPS23,CUEDC1,VEZF1,DYNLL2,OR4D1,EPX,MKS1,SFRS1

chr5 117.2:117.6

chr1 170.8:171.2 C1orf9,FASLG

chr7 135.4:135.6

chr2 126:126.2

chr4 41.4:41.8 DKFZP686A01247,PHOX2B,TMEM33,WDR21B,SLC30A9,CCDC4

chr1 64:64.4 ROR1,UBE2U

chr4 144.4:144.6 USP38,GAB1

chr4 7.6:7.8 AFAP1,SORCS2

chr4 143.8:144.2

chr12 125.4:125.8

chr2 108.2:108.6 SULT1C3,SULT1C1,SULT1C2,GCC2,LIMS1

chr14 68.6:68.8 WDR22,EXDL2,GALNTL1

chr4 84.2:84.4 LIN54,COPS4,PLAC8,HPSE,COQ2

chr3 108.8:109.2 BBX,CD47

chr3 44.6:45 ZNF167,ZNF660,ZNF197,ZNF35,ZNF502,ZNF501,KIAA1143,KIF15,TMEM42,TGM4,ZDHHC3,EXOSC7,CLEC3B

chr15 62:62.2 DAPK2,FAM96A,SNX1,SNX22,PPIB,CSNK1G1

chr7 112:112.4 TMEM168,FLJ31818


chr6 129.4:129.6 LAMA2

chr7 3.8:4.2 SDK1

chr10 55.6:55.8 PCDH15

chr21 16.8:17 C21orf34

chr2 212.8:213.2 ERBB4

chr4 168.8:169.2

chr4 170.8:171 NEK1,CLCN3,C4orf27

chr8 135:135.4

chrX 111:111.2 ZCCHC16,TRPC5

chr17 55.6:55.8 CA4,USP32

chr5 117.8:118

chr6 4.8:5 CDYL,RPP40

chr3 103.6:103.8 ZPLD1


chr20 30:30.4 TTLL9,PDRG1,XKR7,C20orf160,HCK,TM9SF4,PLAGL2,POFUT1,KIF3B,ASXL1

chr1 232.8:233 IRF2BP2


chr6 125.8:126

chr4 191:191.2 DUX4,FRG1,TUBB4Q,DUX4C,FRG2

chr11 60.2:60.4 MS4A8B,MGC35295,MS4A10,CCDC86,GPR44,ZP1,PRPF19,TMEM109,TMEM132A

chr1 8.2:8.6 RERE,SLC45A1

chr4 28.4:28.6

chr2 25.8:26 DTNB,ASXL2,KIF3C

chr4 170.4:170.6 SH3RF1,NEK1

chr15 62.6:62.8 ZNF609,OAZ2,RBPMS2

chr9 13.8:14

chr12 87.6:87.8

chr15 44:44.2

chr12 122.6:122.8 FLJ39378,DDX55,EIF2B1,GTF2H3,C12orf38,ATP6V0A2,DNAH10,TMED2

chrX 110.6:110.8 ALG13

chr3 187.4:187.6 DGKG

BiakaPygmy

BantuEurope

Mideast

S.AsiaE.Asia

Oceania

America

0.05

0.001

Figure 26: The top 1% of XP-EHH signals in East Asia, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.

29

chr22 21.6:21.8 RTDR1,GNAZ,RAB36

chr2 177.8:178.2 HNRPA3,PDE11A,NFE2L2,AGPS,TTC30A,TTC30B

chr22 46.4:46.6 FLJ46257

chr2 178.4:178.8 DRB1,PDE11A,OSBPL6

chr4 158.2:158.6 GLRB,GRIA2

chr10 59.2:59.4chr12 125.4:125.8

chr4 158.8:159chr17 56.2:56.6 BCAS3

chr3 157.2:157.6 KCNAB1


chr10 115:115.4 HABP2,NRAP,CASP7


chr16 11:11.4 PRM1,KIAA0350,SOCS1,TNP2,PRM3,PRM2,C16orf75,LOC400499

chr19 46.6:46.8 TGFB1,MGC4093,EXOSC5,BCKDHA,B3GNT8,FLJ10241,CEACAM21,CEACAM4,TMEM91

chr5 107.2:107.6 FBXL17

chr12 1:1.4 ERC1

chr15 58.2:58.4 ANXA2

chr5 169:169.2 CCDC99,DOCK2

chr6 48.6:49chr12 30.4:30.6chr5 154.6:155chr6 49.2:49.4

chr1 165.2:165.6 C1orf32,MAEL,GPA33,POU2F1,DUSP27

chr2 108.4:108.8 SULT1C2,GCC2,LIMS1,RANBP2,FLJ32745

chr12 26:26.4 RASSF8,BHLHB3,SSPN,ITPR2

chr6 105.8:106.2 PREP

chr7 145.4:145.8 CNTNAP2


chr15 43.8:44.2 SQRDL

chr21 14.8:15 SAMSN1

chr6 111:111.4 CDC2L6,AMD1,C6orf51,BXDC1

chr21 16.2:16.6 USP25,C21orf34

chr5 140.6:141 PCDHB9,PCDHB10,PCDHB11,PCDHB12,PCDHB13,PCDHB14,PCDHB15,SLC25A2,TAF7,PCDHGA1,PCDHGA2,PCDHGA3,PCDHGB1,PCDHGA4,PCDHGB2,PCDHGA5,PCDHGB3,PCDHGA6,PCDHGA7,PCDHGB4,PCDHGA8,PCDHGB5,PCDHGA9,PCDHGB6,PCDHGA10,PCDHGB7,PCDHGA11,PCDHGA12,PCDHGC3,PCDHGC4,PCDHGC5,HDAC3,C5orf16,FCHSD1,CENTD3,DIAPH1

chr5 153.6:153.8 GALNT10,SAP30L,HAND1

chr6 134.6:135chr20 32.6:33 ACSS2,ITCH,DYNLRB1,MAP1LC3A,PIGU,TP53INP2,NCOA6,GSS,MYH7B,GGTL3

chr1 178:178.4 C1orf76,TOR1AIP2,IFRG15,TOR1AIP1,QSCN6,CEP350

chr4 61.4:61.6chr22 39.4:39.8 MKL1,MCHR1,SLC25A17,ST13,XPNPEP3,DNAJB7,RBX1,EP300

chr10 2.8:3chr2 158.8:159.2 LOC130940,PKP4

chr6 35.2:35.4 ANKS1A,TCP11,SCUBE3,ZNF76,DEF6,PPARD


chr5 108:108.2 FER

chr18 11.2:11.4chr22 40:40.2 L3MBTL2,RANGAP1,ZC3H7B,TEF,TOB2,PHF5A,ACO2

chr22 48.2:48.4 FLJ44385,C22orf34

chr5 173.2:173.4 CPEB4,HMP19

chr3 190:190.2 LPP

chr6 125.8:126chr2 3.6:3.8 RNASEH1,RPS7,COLEC11,ALLC

chr2 28.2:28.6 BRE,FOSL2,PLB1

chr10 110:110.2chr9 122.4:122.6 FBXW2,CDK5RAP2,PSMD5,MEGF9

chr6 162:162.2 PARK2


chr11 46.4:46.6 DGKZ,MDK,CHRM4,FLJ20294,C11orf77,KIAA0652

chr3 158:158.2 FLJ16641

chr5 8.6:8.8chr10 59.6:59.8 IPMK,ZCD1,UBE2D1,TFAM

chr4 60.8:61.2chr11 92.8:93 C11orf75,CCDC67

chr2 17.6:18 VSNL1,SMC6,FLJ40869,KCNS3

chr2 9.4:9.8 ITGB1BP1,DDEF2,CPSF3,IAH1,ADAM17,YWHAQ

chr4 160.6:160.8chr5 150.4:150.6 TNIP1,ANXA6,CCDC69,GM2A,SLC36A3,GPX3

chr10 22.8:23 PIP5K2A

chr1 27.6:27.8 FGR,SYTL1,MAP3K6,FCN3,GPR3,WASF2,AHDC1,CD164L2

chr6 54.6:55 FAM83B

chr22 43:43.2chr21 16.8:17 C21orf34

chr4 29.4:29.6chr13 79.4:79.6

chr7 135.4:135.6chr2 161.2:161.4

chr2 27.8:28 SLC4A1AP,RBKS,BRE,MRPL33

chr6 155.6:155.8 TIAM2,TFB1M,CLDN20,NOX3

chr12 87.6:87.8chr11 25.4:25.6

chr19 23:23.2chr3 24:24.2 NR1D2,THRB

chr2 127.8:128 ERCC3,MAP3K2,IWS1,PROC,MYO7B

chr5 134.6:134.8 H2AFY,C5orf20

BiakaPygmy

BantuEurope

Mideast

S.AsiaE.Asia

Oceania

America

0.05

0.001

Figure 27: The top 1% of XP-EHH signals in the Americas, ordered from top to bottom in orderof significance. See the caption of Figure 1 in the main text for details.

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chr22 44.8:45.2 FLJ20699,WNT7B,FLJ27365,PPARA,LOC150383,PKDREJ,GTSE1,TRMU,CELSR1,C22orf26

chr6 105.2:105.6 HACE1,LIN28B

chr12 65.6:66 CAND1

chr21 16.2:16.6 USP25,C21orf34

chr4 95:95.4 ATOH1,SMARCAD1,PGDS

chr8 100:100.4 OSR2,VPS13B

chr8 19.4:19.8 ChGn,INTS10,LPL

chr9 38:38.4 SHB,ALDH1B1,IGFBPL1

chr1 174.8:175.2 ASTN1,PAPPA2

chr5 58.6:59 PDE4D

chr8 134.8:135.2

chr6 105.8:106 PREP

chr4 170.8:171.2 NEK1,CLCN3,C4orf27,MFAP3L,AADAT

chr4 170.2:170.6 CBR4,SH3RF1,NEK1

chr1 113.2:113.6 LRIG2,SLC16A1

chr2 22.2:22.6

chr20 5.8:6 C20orf196,CHGB,CGI−09,MCM8,CRLS1,C20orf75,C20orf42

chr4 55.8:56.2 SRD5A2L,TMEM165,CLOCK,PDCL2,NMU

chr5 59.8:60.2 DEPDC1B,ELOVL7,ERCC8

chr22 24.8:25 MYO18B,SEZ6L

chr4 85.2:85.6 NKX6−1


chr4 95.6:95.8 PDLIM5

chr2 237:237.4 CXCR7,IQCA

chr11 120.6:121 TECTA,SORL1,SC5DL

chr2 20.2:20.6 SDC1,PUM2,RHOB

chr5 59.2:59.6

chr12 116.4:116.6 KSR2

chr21 17.6:17.8 CXADR

chr4 159.6:159.8 RXFP1,LOC201725,PPID,ETFDH

chr11 25.2:25.6

chr11 30.8:31.2 DCDC5,DCDC1

chr2 165.8:166.2 SCN2A,SCN3A,FAM130A2

chr11 31.4:31.8 DPH4,IMMP1L,PAX6,ELP4

chr12 92.8:93 CRADD

chr2 212.8:213.2 ERBB4

chr8 63.6:64 FAM77D

chr4 160:160.4 FLJ25371

chr2 2.8:3.2 TSSC1

chr3 71.4:71.8 FOXP1,EIF4E3

chr17 50.8:51 HLF,MMD

chr2 142.6:143 LRP1B

chr18 11.6:11.8 GNAL,CHMP1B

chr22 40.4:40.6 MEI1,XRCC6,NHP2L1,FLJ23584,CCDC134,SREBF2

chr4 186.6:186.8 ANKRD37,C4orf20,CCDC110,PDLIM3,SORBS2




chr8 100.6:100.8 VPS13B

chr9 0.8:1 DMRT1,DMRT3,DMRT2

chr10 65.6:66

chr16 60:60.2 CDH8

chr5 30.6:30.8

chr13 110.4:110.8 ANKRD10,ARHGEF7,C13orf16

chr7 142:142.2 PRSS1,PRSS2

chr5 170.2:170.6 GABRP,RANBP17

chr10 6.8:7.2 SFMBT2

chr16 5.4:5.6

chr2 205.8:206 PARD3B

chr16 77.2:77.4 WWOX

chr11 44:44.2 LOC390110,PHACS,EXT2,ALX4

chr18 11.2:11.4

chr3 179.2:179.4

chr2 64.2:64.4 PELI1

chr8 99.6:99.8 STK3

chr22 39.8:40.2 EP300,L3MBTL2,RANGAP1,ZC3H7B,TEF,TOB2,PHF5A,ACO2

chr2 126:126.2

chr21 16.8:17 C21orf34

chr1 203.4:203.8 RBBP5,RIPK5,TMCC2,NUAK2,KLHDC8A,LEMD1,PCTK3,MFSD4

chr13 43.6:43.8 C13orf21

chr8 64.6:64.8

chrX 110.6:110.8 ALG13

chr10 9:9.2

chr5 99.4:99.6

chr2 232.2:232.4 MGC35154,PTMA,PDE6D,COPS7B

chr20 0:0.2 DEFB125,DEFB126,DEFB127,DEFB128,DEFB129,DEFB32,C20orf96,ZCCHC3

BiakaPygmy

BantuEurope

Mideast

S.AsiaE.Asia

Oceania

America

0.05

0.001

Figure 28: The top 1% of XP-EHH signals in Oceania, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.

31

References

[1] Clark AG, Hubisz MJ, Bustamante CD, Williamson SH, Nielsen R (2005) Ascertainment biasin studies of human genome-wide polymorphism. Genome Res 15: 1496–1502.

[2] Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, et al. (2007) Genome-wide detectionand characterization of positive selection in human populations. Nature 449: 913–918.

[3] Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ, et al. (2005) Calibrating a coalescentsimulation of human genome sequence variation. Genome Res 15: 1576–1583.

[4] Tang K, Thornton K, Stoneking M (2007) A New Approach for Using Genome Scans to DetectRecent Positive Selection in the Human Genome. PLoS Biol 5: e171.

[5] Teshima KM, Coop G, Przeworski M (2006) How reliable are empirical genomic scans forselective sweeps? Genome Res 16: 702–712.

[6] Thornton KR, Jensen JD (2007) Controlling the false-positive rate in multilocus genome scansfor selection. Genetics 175: 737–750.

[7] Voight BF, Kudaravalli S, Wen X, Pritchard JK (2006) A map of recent positive selection inthe human genome. PLoS Biol 4: e72.

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