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Table 2 Top SNPs and corresponding genes identified using the SGB approach

From: Rare variant collapsing in conjunction with mean log p-value and gradient boosting approaches applied to Genetic Analysis Workshop 17 data

 

Top SNPs identified (from highest to lowest variable importance)

SNPs

C13S523

C9S3621

C6S6142

C5S237

C9S4860

C22S1374

C2S5630

C11S60

 

C13S905

C1S6542

C7S2893

C19S282

C6S1097

C10S2632

C2S955

C14S784

 

C1S5779

C7S2446

C9S1469

C12S4668

C2S1087

C2S2148

C1S10506

C6S2129

 

C15S3343

C12S4188

C14S1863

C2S4601

C6S2469

C10S2533

C19S609

C10S5515

 

C1S5530

C17S3017

C9S1225

C13S522

C12S3028

C5S3461

C19S1762

C1S9584

 

C19S1849

C9S4013

C22S1405

C12S622

C12S7056

C2S7558

C16S3421

C12S552

 

C2S4407

C1S996

C22S1351

C20S2310

C22S1158

C15S4060

C17S1262

C3S1305

 

C7S158

C10S387

C17S2377

C7S1877

C1S9718

C10S4422

C4S2872

C7S3971

 

C2S689

C8S3322

C10S6566

C14S20

C7S1076

C11S3224

C1S7413

C22S146

 

C8S4238

C8S4028

C18S2322

C6S6040

C12S5220

C6S6177

C19S3382

C19S2528

 

C1S9506

C4S4283

C12S3528

C11S2585

C17S2376

C12S5446

C17S4841

C1S10200

 

C4S2239

C7S3613

C5S4072

C11S6503

C11S4881

C1S10800

C9S123

C2S7414

 

C2S1139

C3S3962

C7S3490

C10S5783

C11S1683

C9S2613

C11S2532

C7S4111

 

C18S2310

C2S4079

C6S2366

C8S627

C2S6985

C1S7941

C11S5292

C4S4339

 

C3S3938

C6S5380

C22S875

C1S7092

C7S2590

C11S2871

C6S2216

C6S5677

 

C7S4646

C8S850

C8S271

C4S2296

C10S386

C9S5111

C15S3138

C1S7427

 

C17S3510

C3S96

C22S385

C1S3900

C3S4638

C21S672

C1S1388

C10S2683

 

C13S1168

C7S3697

C2S4909

C11S1280

C2S2154

C12S4591

C3S1176

C22S2039

 

C11S3320

C2S873

C9S3100

C2S7390

C12S5526

C11S1599

C6S4552

C1S10256

 

C10S3243

C12S5510

C4S2678

C4S2970

C2S8207

C16S560

C6S7138

C17S321

 

C20S1844

C12S5445

C10S2670

C1S4009

C17S2026

C9S3554

C13S1660

C14S590

 

C10S6432

C9S759

C19S4625

C1S9511

C8S934

C6S4242

C18S1560

C4S97

 

C15S3744

C7S397

C19S4658

C12S4534

C9S2083

C19S5271

C7S3898

C1S4838

 

C9S1607

C4S3834

C11S5644

C15S2848

C10S3777

C3S3657

C14S122

C14S3426

 

C16S1482

C4S3076

C9S2542

C2S6995

C21S778

C9S1835

C15S3559

C8S3416

 

C5S2032

C1S10813

C10S5690

C1S3676

C6S4400

C13S163

C22S645

C12S3039

 

C1S10164

C6S7164

C22S1222

C4S649

C19S277

C1S7408

C1S1542

C4S186

Genes

TNFRSF25

AHSA2

ADH1B

GPR85

OR13C5

SYTL2

PSME2

PTPRS

 

ARHGEF10L

RGPD3

C4ORF33

PTPRZ1

CDK5RAP2

PDGFD

VTI1B

OR10H3

 

KIF17

RGPD4

TKTL2

PAX4

STOM

EXPH5

BEGAIN

CYP4F2

 

PDE4B

ACVR1C

ANP32C

SMO

GOLGA1

OR8D4

PAQR5

ZNF486

 

PTGER3

LY75

PLEKHG4B

ZC3HC1

BRD3

CLEC2D

TSPAN3

NPHS1

 

MSH4

PPIG

ZNF474

AKR1B1

CARD9

KLRK1

ADAMTS7

ZNF576

 

STXBP3

WDR75

ABLIM3

SLC37A3

ECHDC3

OR6C1

ALPK3

LYPD5TMC4

 

HIPK1

LOC729332

FOXI1

GATA4

ERCC6

OR6C65

SLC28A1

C20ORF32

 

VTCN1

UGT1A10

PGBD1

TNFRSF10D

PGBD3

SRGAP1

AKAP13

PRIC285

 

ARNT

COL6A3

BAT2

CDCA2

HKDC1

PLXNC1

ZNF213

PIGP

 

ADAM15

MTERFD2

SLC44A4

PTK2B

MAT1A

C12ORF63

USP31

ETS2

 

OR10J1

CRELD1

PSMB8

EXT1

CYP2C8

CHPT1

LOC100132786

HIRA

 

OR10J5

LOC100130135

MDN1

SAMD12

SORCS1

TRAFD1

TRPV3

ARVCF

 

UAP1

SETD2

VNN1

MLZE

CASP7

CAMKK2

KCNJ12

TOP3B

 

LRRN2

GOLGB1

FUCA2

TG

DCLRE1A

ANAPC5

SLFN13

SUSD2

 

NUAK2

TMCC1

UTRN

ANKRD15

TACC2

ZNF26

PIP4K2B

SEC14L3

 

IKBKE

TRPC1

AGPAT4

PDCD1LG2

ATHL1

TNFRSF19

BRCA1

SMTN

 

LAMB3

CRIPAK

PMS2

AQP3

GALNTL4

FLT1

FAM117A

LIMK2

 

DUSP10

GRK4

TSPAN13

C9ORF131

HPS5

TRPC4

RECQL5

LOC100132621

 

KIAA0133

AFAP1

NPC1L1

NPR2

NELL1

FREM2

HRH4

 
 

ARL6IP2

PF4V1

NCF1

POLR1E

OR8H1

PIBF1

B4GALT6

 
 

OXER1

STBD1

FBXO24

SMC5

OR9G4

RNASE6

MCART2

 
 

FSHR

FAM13A1

FBXL13

C9ORF79

OR4D9

FLJ10357

ZNF57

 
 

BCL11A

PDLIM5

RELN

ROR2

AHNAK

ACIN1

ZNF77

 
  1. Boldface indicates results that match the simulated model.