Variant report

Variant	rs9837237
Chromosome Location	chr3:49215583-49215584
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49210011..49212298-chr3:49215313..49217112,2	MCF-7	breast:
2	chr3:49136133..49137781-chr3:49215466..49218025,2	K562	blood:
3	chr3:49214354..49216613-chr3:49252087..49254601,2	K562	blood:
4	chr3:49210124..49212449-chr3:49213139..49215737,4	K562	blood:
5	chr3:49201068..49204007-chr3:49213052..49215729,2	K562	blood:
6	chr3:49131687..49134642-chr3:49213919..49216265,2	K562	blood:

Variant related genes	Relation type
ENSG00000172053	Chromatin interaction
ENSG00000177352	Chromatin interaction
ENSG00000185909	Chromatin interaction
ENSG00000198218	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10049462	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10154895	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10865954	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11130182	0.85[ASN][1000 genomes]
rs11130184	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1134043	0.93[CEU][hapmap]
rs11552724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11706052	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11706189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11710247	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11712006	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11713297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11715581	0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11716334	0.89[ASN][1000 genomes]
rs11716445	0.92[CEU][hapmap]
rs11716614	0.92[CEU][hapmap]
rs11718982	0.88[EUR][1000 genomes]
rs11719220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11719457	0.81[EUR][1000 genomes]
rs11720460	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11920267	1.00[JPT][hapmap]
rs12487580	0.87[ASN][1000 genomes]
rs12490393	0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12493001	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12629759	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12631989	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12636030	0.97[ASN][1000 genomes]
rs12637576	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12715434	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13064784	0.87[ASN][1000 genomes]
rs13068038	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13072554	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13077498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13080725	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13086240	0.81[EUR][1000 genomes]
rs13087930	0.81[EUR][1000 genomes]
rs13090839	0.81[EUR][1000 genomes]
rs13096406	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2117938	1.00[JPT][hapmap]
rs2304442	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs3212	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34326553	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34343820	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34504524	0.84[EUR][1000 genomes]
rs34509487	0.81[EUR][1000 genomes]
rs34566463	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34580506	1.00[CEU][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34784192	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34889065	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35060561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35102816	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35108630	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35174559	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs35185152	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35283189	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35673421	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3923475	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4279134	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4308307	0.90[ASN][1000 genomes]
rs4364202	0.85[ASN][1000 genomes]
rs4499638	0.95[ASN][1000 genomes]
rs4513485	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4521268	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4536858	0.95[ASN][1000 genomes]
rs4955410	1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4955418	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4955419	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4955420	0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4955432	1.00[JPT][hapmap]
rs4974080	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs5030795	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55713230	0.95[ASN][1000 genomes]
rs55921200	0.83[EUR][1000 genomes]
rs56306491	0.87[EUR][1000 genomes]
rs56318350	0.81[EUR][1000 genomes]
rs61583136	0.92[ASN][1000 genomes]
rs62262517	0.85[ASN][1000 genomes]
rs6414613	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6446205	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs66991555	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67286839	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6770112	0.92[ASN][1000 genomes]
rs6779394	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6781790	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs67831908	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6784111	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6790914	0.95[ASN][1000 genomes]
rs6794924	0.89[ASN][1000 genomes]
rs6795025	0.84[ASN][1000 genomes]
rs71324939	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73084135	0.92[EUR][1000 genomes]
rs7432989	1.00[CHD][hapmap]
rs7615235	0.84[ASN][1000 genomes]
rs7621015	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7626445	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7652746	1.00[JPT][hapmap]
rs9311439	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9814987	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9826525	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9828310	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9835439	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9837625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840050	1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs9844757	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs9846123	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9847839	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9850917	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9855123	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9862483	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9880088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9880309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9990153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs9837237	WDR6	cis	Artery Tibial	GTEx
rs9837237	C3orf62	cis	cerebellum	SCAN
rs9837237	CSPG5	cis	parietal	SCAN
rs9837237	ALAS1	cis	cerebellum	SCAN
rs9837237	HEMK1	cis	parietal	SCAN
rs9837237	COL7A1	cis	parietal	SCAN
rs9837237	WDR6	cis	cerebellum	SCAN
rs9837237	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9837237	WDR6	cis	Esophagus Mucosa	GTEx
rs9837237	RNF123	cis	parietal	SCAN
rs9837237	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs9837237	WDR6	cis	Adipose Subcutaneous	GTEx
rs9837237	CCDC36	cis	cerebellum	SCAN
rs9837237	KBTBD3	trans	parietal	SCAN
rs9837237	NICN1	cis	cerebellum	SCAN
rs9837237	WDR6	cis	Whole Blood	GTEx
rs9837237	WDR6	cis	parietal	SCAN
rs9837237	ARIH2	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49211200-49218800	Weak transcription	Fetal Kidney	kidney
2	chr3:49211200-49224600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:49211400-49216000	Weak transcription	Brain Substantia Nigra	brain
4	chr3:49211400-49217600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:49211800-49216000	Genic enhancers	Fetal Muscle Trunk	muscle
6	chr3:49211800-49216200	Genic enhancers	Fetal Muscle Leg	muscle
7	chr3:49211800-49216600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:49212000-49216200	Weak transcription	Osteobl	bone
9	chr3:49212200-49218800	Weak transcription	HepG2	liver
10	chr3:49212400-49215600	Strong transcription	Lung	lung
11	chr3:49212600-49216400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:49212800-49215600	Strong transcription	Aorta	Aorta
13	chr3:49212800-49215800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr3:49212800-49216200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:49212800-49217000	Strong transcription	Fetal Stomach	stomach
16	chr3:49213000-49217200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:49213200-49215800	Strong transcription	Spleen	Spleen
18	chr3:49213400-49216000	Strong transcription	Fetal Intestine Small	intestine
19	chr3:49213400-49217600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:49213400-49217800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:49213600-49215600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:49213800-49215600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:49213800-49216000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:49213800-49216000	Strong transcription	Ovary	ovary
25	chr3:49213800-49217200	Enhancers	Fetal Heart	heart
26	chr3:49213800-49217400	Weak transcription	Fetal Brain Female	brain
27	chr3:49214000-49215600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:49214000-49215800	Weak transcription	Primary T cells from cord blood	blood
29	chr3:49214000-49216200	Strong transcription	Stomach Smooth Muscle	stomach
30	chr3:49214000-49217400	Weak transcription	Gastric	stomach
31	chr3:49214000-49218000	Weak transcription	Brain Germinal Matrix	brain
32	chr3:49214000-49218800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:49214000-49219200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:49214000-49221400	Weak transcription	Liver	Liver
35	chr3:49214000-49224600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:49214200-49215800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:49214200-49216000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:49214200-49216000	Weak transcription	Colonic Mucosa	Colon
39	chr3:49214200-49217200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:49214200-49217600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:49214200-49218000	Weak transcription	Colon Smooth Muscle	Colon
42	chr3:49214200-49220800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:49214200-49224000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:49214400-49216200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:49214400-49216800	Enhancers	Left Ventricle	heart
46	chr3:49214400-49217200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:49214400-49217800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:49214600-49216200	Weak transcription	Placenta	Placenta
49	chr3:49214800-49216000	Enhancers	Right Atrium	heart
50	chr3:49214800-49217800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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