Skip to main content

Table 3 Examples of top outlier peak regions for each population

From: hzAnalyzer: detection, quantification, and visualization of contiguous homozygosity in high-density genotyping datasets

Pop.

Chr

Position

Low valley

High valley

Pk.Ht.

SNPct

W(bp)

W(cm)

Extentmin

Freqhap-max

Top 5 gene(s)

GeneCt

YRI

11

48,984,887

46,179,339

51,434,161

0.7583

2,260

5,254,822

7.1256

1,944,689

0.2966

BC142657, C11orf49, AMBRA1, PTPRJ, CKAP5

48

 

X

64,291,347

62,718,942

66,950,662

0.5043

1,283

4,231,720

4.8877

1,706,793

0.2045

AR, MTMR8, ARHGEF9, HEPH, MSN

12

 

19

21,348,594

20,644,142

21,607,663

0.476

728

963,521

2.0049

278,309

0.4492

ZNF431, ZNF714, ZNF708, ZNF430, ZNF429

8

 

15

42,487,755

40,203,270

42,922,650

0.4277

1,542

2,719,380

4.4896

280,917

0.6695

FRMD5, TTBK2, UBR1, CASC4, TP53BP1

47

 

13

56,734,306

54,206,759

58,262,174

0.3587

3,933

4,055,415

5.588

543,152

0.4322

PCDH17, PRR20

2

 

1

172,725,722

171,321,975

173,400,872

0.3306

1,303

2,078,897

2.7759

1,077,265

0.2288

RABGAP1L, SLC9A11, TNN, KLHL20, RC3H1

16

 

3

49,131,477

46,848,671

51,894,338

0.3307

1,993

5,045,667

6.1529

646,401

0.3729

DOCK3, MAP4, SMARCC1, CACNA2D2, RBM6

108

 

14

66,177,344

65,574,279

67,039,563

0.3157

901

1,465,284

2.1116

451,154

0.3814

GPHN, MPP5, FAM71D, C14orf83, EIF2S1

7

 

2

62,928,490

62,640,536

64,139,379

0.3138

864

1,498,843

1.9062

665,460

0.3898

LOC51057, EHBP1, VPS54, UGP2, MDH1

7

 

16

34,336,349

34,040,995

35,126,826

0.2836

446

1,085,831

1.8457

407,250

0.3559

No overlapping gene symbols

0

CEU

X

56,905,680

54,032,865

58,499,973

2.2637

1,588

4,467,108

7.0248

2,146,728

0.6705

FAAH2, WNK3, FAM120C, PFKFB1, PHF8

30

 

4

33,984,210

32,226,578

34,781,662

1.1807

1,754

2,555,084

3.6574

1,063,099

0.5847

No overlapping gene symbols

0

 

10

74,474,938

73,363,734

76,877,918

1.1538

1,994

3,514,184

4.2036

1,225,977

0.5847

ADK, CBARA1, MYST4, CCDC109A, VCL

45

 

17

56,029,088

54,786,548

56,697,157

1.1855

950

1,910,609

2.8676

650,495

0.7542

BCAS3, USP32, TMEM49, APPBP2, CLTC

17

 

11

47,998,372

46,181,418

51,434,161

1.021

2,256

5,252,743

7.1227

2,476,725

0.3898

BC142657, C11orf49, AMBRA1, PTPRJ, CKAP5

48

 

2

136,299,164

134,916,186

137,368,521

0.8663

2,261

2,452,335

2.5254

983,710

0.7373

ZRANB3, TMEM163, R3HDM1, RAB3GAP1, DARS

13

 

12

33,861,148

32,686,226

38,560,061

0.8322

3,319

5,873,835

10.0596

1,347,796

0.3898

CPNE8, KIF21A, SLC2A13, PKP2, C12orf40

12

 

6

28,454,924

26,007,118

30,140,896

0.829

4,884

4,133,778

5.9709

1,925,294

0.1102

AK309286, GABBR1, ZNF322A, ZNF184, TRIM38

116

 

1

35,416,859

35,088,324

36,679,373

0.8304

716

1,591,049

1.9898

957,224

0.6525

ZMYM4, EIF2C3, KIAA0319L, THRAP3, EIF2C4

27

 

15

41,082,380

40,198,534

43,641,969

0.8478

2,088

3,443,435

5.6849

620,196

0.5424

FRMD5, TTBK2, UBR1, CASC4, TP53BP1

60

CHB

X

65,578,703

62,500,211

68,093,466

5.0603

1,811

5,593,255

6.4603

3,865,015

1

OPHN1, AR, MTMR8, ARHGEF9, HEPH

16

 

16

46,816,951

45,019,628

47,582,293

1.7237

1,197

2,562,665

4.3969

1,239,919

0.5682

ITFG1, PHKB, LONP2, FLJ43980, N4BP1

16

 

3

49,185,837

46,688,461

52,084,708

1.7352

2,120

5,396,247

6.5804

1,411,092

0.7614

DOCK3, MAP4, SMARCC1, CACNA2D2, RBM6

124

 

20

33,906,145

31,887,721

34,457,027

1.1757

1,515

2,569,306

4.7755

641,849

0.6477

PHF20, ITCH, PIGU, NCOA6, UQCC

44

 

17

56,257,611

54,786,430

56,802,151

1.0563

1,040

2,015,721

3.0254

563,530

0.7159

BCAS3, USP32, TMEM49, APPBP2, CLTC

17

 

1

50,585,736

48,934,817

53,018,060

1.0833

2,299

4,083,243

5.1065

1,010,684

0.5227

AGBL4, FAF1, ZFYVE9, OSBPL9, EPS15

25

 

2

72,358,317

72,139,001

73,325,161

1.0369

914

1,186,160

1.5085

785,525

0.8523

EXOC6B, SFXN5, RAB11FIP5, EMX1, CYP26B1

10

 

15

61,947,157

61,420,087

63,327,879

1.0094

1,241

1,907,792

3.1497

757,196

0.6136

HERC1, CSNK1G1, ZNF609, DAPK2, USP3

27

 

5

43,332,643

41,569,404

46,432,729

0.9655

3,211

4,863,325

7.1409

940,407

0.3182

HCN1, GHR, OXCT1, NNT, MGC42105

18

 

4

33,761,093

32,224,418

34,856,502

0.9703

1,854

2,632,084

3.7676

705,955

0.4773

No overlapping gene symbols

0

JPT

X

65,574,377

62,541,924

68,119,789

4.6884

1,830

5,577,865

6.4425

2,974,147

1

OPHN1, AR, MTMR8, ARHGEF9, HEPH

16

 

3

49,116,120

46,984,286

52,086,091

1.5554

1,926

5,101,805

6.2214

1,411,982

0.6744

DOCK3, MAP4, SMARCC1, CACNA2D2, RBM6

117

 

16

46,405,964

45,019,628

47,589,442

1.4543

1,203

2,569,814

4.4092

1,013,458

0.6512

ITFG1, PHKB, LONP2, FLJ43980, N4BP1

16

 

11

51,354,159

45,478,264

51,434,161

1.1994

2,899

5,955,897

8.0762

1,844,210

0.3837

BC142657, C11orf49, AMBRA1, PHF21A, PTPRJ

57

 

1

50,634,574

49,236,023

52,884,998

1.1586

1,797

3,648,975

4.5634

727,447

0.7442

AGBL4, FAF1, ZFYVE9, OSBPL9, EPS15

22

 

20

33,684,569

31,842,856

34,417,872

1.0984

1,512

2,575,016

4.7861

982,049

0.4186

PHF20, ITCH, PIGU, NCOA6, UQCC

45

 

2

72,358,024

71,951,517

73,081,576

1.0483

956

1,130,059

1.4372

771,138

0.8721

EXOC6B, SFXN5, EMX1, CYP26B1, SPR

5

 

15

62,853,070

61,443,788

63,335,076

1.0036

1,219

1,891,288

3.1224

868,839

0.5465

HERC1, CSNK1G1, ZNF609, DAPK2, USP3

27

 

14

65,950,544

65,443,441

67,097,562

0.9667

1,112

1,654,121

2.3838

987,976

0.407

GPHN, MPP5, C14orf83, FAM71D, PLEKHH1

9

 

17

55,887,456

53,750,682

56,801,264

0.9595

1,451

3,050,582

4.5786

555,447

0.8023

BCAS3, PPM1E, USP32, TEX14, TMEM49

33

  1. Outlier peak regions were sorted by peak height and ten representative examples chosen from the top. Columns with abbreviated names not referred to in the text are: Pop., population; Chr, chromosome; Pk. Ht, peak region height; SNPct, number of SNPs in region; W(bp), peak region width in base pairs; W(cm), peak region width in centimorgans; GeneCt, number of genes in region. Genes listed are sorted by length and the top five shown.
Back to article page

Genome Biology

ISSN: 1474-760X

Contact us