Variant report

Variant	rs11713297
Chromosome Location	chr3:49213030-49213031
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49158589..49160627-chr3:49212099..49214336,2	K562	blood:
2	chr3:49207629..49210061-chr3:49211282..49215140,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185909	Chromatin interaction
ENSG00000172037	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:115)

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];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10154895	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865954	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11130182	0.88[ASN][1000 genomes]
rs11130184	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1134043	0.93[CEU][hapmap]
rs11552724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[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];0.81[ASN][1000 genomes]
rs11706189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710247	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11712006	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11715581	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11716334	0.87[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];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11719457	0.81[EUR][1000 genomes]
rs11720460	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11920267	1.00[JPT][hapmap]
rs12487580	0.90[ASN][1000 genomes]
rs12490393	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12493001	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12629759	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12631989	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12636030	1.00[ASN][1000 genomes]
rs12637576	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12715434	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13064784	0.85[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];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13072554	0.85[EUR][1000 genomes];0.81[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];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13080725	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13086240	0.81[EUR][1000 genomes]
rs13087930	0.81[EUR][1000 genomes]
rs13090839	0.81[EUR][1000 genomes]
rs13096406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[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];0.85[ASN][1000 genomes]
rs34326553	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34343820	0.90[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];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][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];0.89[ASN][1000 genomes]
rs34784192	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34889065	0.84[EUR][1000 genomes];0.89[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];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35102816	0.84[EUR][1000 genomes]
rs35108630	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35174559	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs35185152	0.90[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];0.89[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];0.89[ASN][1000 genomes]
rs3923475	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4279134	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4308307	0.92[ASN][1000 genomes]
rs4364202	0.83[ASN][1000 genomes]
rs4499638	0.97[ASN][1000 genomes]
rs4513485	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4521268	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4536858	0.97[ASN][1000 genomes]
rs4955410	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4955418	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4955419	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4955420	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[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];0.89[ASN][1000 genomes]
rs55713230	0.97[ASN][1000 genomes]
rs55921200	0.83[EUR][1000 genomes]
rs56306491	0.87[EUR][1000 genomes]
rs56318350	0.81[EUR][1000 genomes]
rs61583136	0.95[ASN][1000 genomes]
rs62262517	0.83[ASN][1000 genomes]
rs6414613	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6446205	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs66991555	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67286839	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6770112	0.95[ASN][1000 genomes]
rs6779394	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6781790	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs67831908	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6784111	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6790914	0.97[ASN][1000 genomes]
rs6794924	0.87[ASN][1000 genomes]
rs6795025	0.81[ASN][1000 genomes]
rs71324939	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73084135	0.92[EUR][1000 genomes]
rs7432989	1.00[CHD][hapmap]
rs7615235	0.82[ASN][1000 genomes]
rs7621015	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7626445	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7652746	1.00[JPT][hapmap]
rs9311439	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[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];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9818758	0.82[YRI][hapmap]
rs9826525	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9828310	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9835439	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9837237	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]
rs9837625	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840050	1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs9844757	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.82[YRI][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];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9848772	0.82[YRI][hapmap]
rs9850917	1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9855123	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9862483	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873994	0.82[YRI][hapmap]
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];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9990153	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs11713297	WDR6	cis	Esophagus Mucosa	GTEx
rs11713297	HEMK1	cis	parietal	SCAN
rs11713297	RNF123	cis	parietal	SCAN
rs11713297	CSPG5	cis	parietal	SCAN
rs11713297	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs11713297	CCDC36	cis	cerebellum	SCAN
rs11713297	USP4	cis	multi-tissue	Pritchard
rs11713297	ARIH2	cis	cerebellum	SCAN
rs11713297	WDR6	cis	cerebellum	SCAN
rs11713297	WDR6	cis	parietal	SCAN
rs11713297	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs11713297	ALAS1	cis	cerebellum	SCAN
rs11713297	C3orf62	cis	cerebellum	SCAN
rs11713297	WDR6	cis	Whole Blood	GTEx
rs11713297	KBTBD3	trans	parietal	SCAN
rs11713297	WDR6	cis	Adipose Subcutaneous	GTEx
rs11713297	WDR6	cis	multi-tissue	Pritchard
rs11713297	NICN1	cis	cerebellum	SCAN
rs11713297	WDR6	cis	Artery Tibial	GTEx
rs11713297	COL7A1	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49209600-49213800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:49209800-49215000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:49210400-49213800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:49210800-49214600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:49211000-49215200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:49211200-49213800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:49211200-49214200	Weak transcription	A549	lung
8	chr3:49211200-49214600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr3:49211200-49218800	Weak transcription	Fetal Kidney	kidney
10	chr3:49211200-49224600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:49211400-49213800	Weak transcription	HUVEC	blood vessel
12	chr3:49211400-49214400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:49211400-49214400	Genic enhancers	Left Ventricle	heart
14	chr3:49211400-49215000	Weak transcription	NHDF-Ad	bronchial
15	chr3:49211400-49216000	Weak transcription	Brain Substantia Nigra	brain
16	chr3:49211400-49217600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:49211600-49213200	Genic enhancers	Spleen	Spleen
18	chr3:49211600-49213600	Enhancers	Right Atrium	heart
19	chr3:49211600-49214000	Strong transcription	Primary T cells from cord blood	blood
20	chr3:49211600-49214000	Strong transcription	Liver	Liver
21	chr3:49211600-49214200	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:49211600-49214400	Strong transcription	Esophagus	oesophagus
23	chr3:49211600-49214800	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr3:49211600-49215200	Genic enhancers	Adipose Nuclei	Adipose
25	chr3:49211800-49213200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:49211800-49213200	Genic enhancers	Fetal Intestine Large	intestine
27	chr3:49211800-49213400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:49211800-49213800	Genic enhancers	Ovary	ovary
29	chr3:49211800-49213800	Strong transcription	Pancreas	Pancrea
30	chr3:49211800-49214000	Strong transcription	NHLF	lung
31	chr3:49211800-49214400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:49211800-49214800	Weak transcription	K562	blood
33	chr3:49211800-49215000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:49211800-49215000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:49211800-49215000	Genic enhancers	Right Ventricle	heart
36	chr3:49211800-49216000	Genic enhancers	Fetal Muscle Trunk	muscle
37	chr3:49211800-49216200	Genic enhancers	Fetal Muscle Leg	muscle
38	chr3:49211800-49216600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:49212000-49213200	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:49212000-49213400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:49212000-49213400	Genic enhancers	Fetal Intestine Small	intestine
42	chr3:49212000-49213600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr3:49212000-49213800	Weak transcription	HSMM	muscle
44	chr3:49212000-49214000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:49212000-49214200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:49212000-49214200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:49212000-49214400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
48	chr3:49212000-49215200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:49212000-49215400	Weak transcription	Brain Angular Gyrus	brain
50	chr3:49212000-49216200	Weak transcription	Osteobl	bone

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