Variant report

Variant	rs62262517
Chromosome Location	chr3:49134914-49134915
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49128926..49138937-chr3:49145476..49160975,31	K562	blood:
2	chr3:49134791..49138406-chr3:49156749..49159761,5	K562	blood:
3	chr3:49055445..49060745-chr3:49128874..49135153,17	MCF-7	breast:
4	chr3:49131736..49133437-chr3:49134322..49137083,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198218	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000172046	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10154895	0.83[ASN][1000 genomes]
rs10865954	0.88[ASN][1000 genomes]
rs11130182	0.81[ASN][1000 genomes]
rs11130184	0.85[ASN][1000 genomes]
rs11552724	0.93[ASN][1000 genomes]
rs11706052	0.80[ASN][1000 genomes]
rs11706189	0.83[ASN][1000 genomes]
rs11712006	0.93[ASN][1000 genomes]
rs11713297	0.83[ASN][1000 genomes]
rs11715581	0.85[ASN][1000 genomes]
rs11716334	0.85[ASN][1000 genomes]
rs12487580	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12490393	0.85[ASN][1000 genomes]
rs12491743	0.83[AMR][1000 genomes]
rs12493001	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12629759	0.85[ASN][1000 genomes]
rs12636030	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12637037	0.84[EUR][1000 genomes]
rs13064784	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13072554	0.80[ASN][1000 genomes]
rs13080725	0.80[ASN][1000 genomes]
rs13316620	0.80[EUR][1000 genomes]
rs3212	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34326553	0.93[ASN][1000 genomes]
rs34580506	0.93[ASN][1000 genomes]
rs34889065	0.93[ASN][1000 genomes]
rs35108630	0.80[ASN][1000 genomes]
rs35283189	0.93[ASN][1000 genomes]
rs35673421	0.93[ASN][1000 genomes]
rs3923475	0.80[ASN][1000 genomes]
rs4072859	0.83[EUR][1000 genomes]
rs4279134	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4308307	0.85[ASN][1000 genomes]
rs4364202	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4499638	0.80[ASN][1000 genomes]
rs4513485	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4521268	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4536858	0.80[ASN][1000 genomes]
rs4955410	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4955418	0.80[ASN][1000 genomes]
rs4955419	0.85[ASN][1000 genomes]
rs4955420	0.85[ASN][1000 genomes]
rs4974080	0.83[EUR][1000 genomes]
rs5030795	0.93[ASN][1000 genomes]
rs55713230	0.80[ASN][1000 genomes]
rs61583136	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6414613	0.82[EUR][1000 genomes]
rs6446205	0.83[EUR][1000 genomes]
rs66991555	0.88[ASN][1000 genomes]
rs6770112	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6779394	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6781790	0.83[EUR][1000 genomes]
rs6784111	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6789285	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6790914	0.80[ASN][1000 genomes]
rs6795025	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7373790	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7432989	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7615235	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7621015	0.81[EUR][1000 genomes]
rs7626445	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7645551	0.82[EUR][1000 genomes]
rs8926	0.81[EUR][1000 genomes]
rs9814987	0.88[ASN][1000 genomes]
rs9835439	0.83[ASN][1000 genomes]
rs9837237	0.85[ASN][1000 genomes]
rs9837625	0.85[ASN][1000 genomes]
rs9840050	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9846123	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9855123	0.83[ASN][1000 genomes]
rs9862483	0.83[ASN][1000 genomes]
rs9880088	0.83[ASN][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	nsv876765	chr3:49119063-49160671	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs62262517	WDR6	cis	Whole Blood	GTEx
rs62262517	WDR6	cis	lung	GTEx
rs62262517	NICN1	cis	Thyroid	GTEx
rs62262517	NCKIPSD	cis	Muscle Skeletal	GTEx
rs62262517	NCKIPSD	cis	Whole Blood	GTEx
rs62262517	WDR6	cis	Muscle Skeletal	GTEx
rs62262517	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs62262517	NICN1-AS1	cis	Thyroid	GTEx
rs62262517	WDR6	cis	Esophagus Mucosa	GTEx
rs62262517	AMT	cis	Whole Blood	GTEx
rs62262517	WDR6	cis	Esophagus Muscularis	GTEx
rs62262517	AMT	cis	Artery Aorta	GTEx
rs62262517	WDR6	cis	Heart Left Ventricle	GTEx
rs62262517	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs62262517	WDR6	cis	Nerve Tibial	GTEx
rs62262517	AMT	cis	Thyroid	GTEx
rs62262517	WDR6	cis	Adipose Subcutaneous	GTEx
rs62262517	WDR6	cis	Artery Tibial	GTEx
rs62262517	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs62262517	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs62262517	NCKIPSD	cis	Nerve Tibial	GTEx
rs62262517	CCDC36	cis	Artery Tibial	GTEx
rs62262517	AMT	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49132400-49135000	Weak transcription	Fetal Brain Female	brain
2	chr3:49132400-49135200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:49132400-49135200	Weak transcription	Colonic Mucosa	Colon
4	chr3:49132400-49135200	Weak transcription	Gastric	stomach
5	chr3:49132400-49135200	Weak transcription	Ovary	ovary
6	chr3:49132400-49135200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:49132400-49135200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:49132400-49135200	Weak transcription	Small Intestine	intestine
9	chr3:49132400-49135200	Weak transcription	A549	lung
10	chr3:49132400-49135200	Weak transcription	HSMM	muscle
11	chr3:49132400-49135400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:49132400-49135400	Weak transcription	Primary T cells from cord blood	blood
13	chr3:49132400-49135400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:49132400-49135400	Weak transcription	Aorta	Aorta
15	chr3:49132400-49135400	Weak transcription	Brain Substantia Nigra	brain
16	chr3:49132400-49135400	Weak transcription	Fetal Kidney	kidney
17	chr3:49132400-49135600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:49132400-49136000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:49132400-49136800	Weak transcription	Fetal Brain Male	brain
20	chr3:49132400-49136800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:49132400-49140800	Weak transcription	Right Atrium	heart
22	chr3:49132400-49141600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr3:49132600-49135000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:49132600-49135000	Weak transcription	Brain Anterior Caudate	brain
25	chr3:49132600-49135200	Weak transcription	Primary B cells from cord blood	blood
26	chr3:49132600-49135200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr3:49132600-49135200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr3:49132600-49135200	Weak transcription	Fetal Lung	lung
29	chr3:49132600-49135200	Weak transcription	HMEC	breast
30	chr3:49132600-49135200	Weak transcription	NHDF-Ad	bronchial
31	chr3:49132600-49135400	Weak transcription	Brain Angular Gyrus	brain
32	chr3:49132600-49135400	Weak transcription	Esophagus	oesophagus
33	chr3:49132600-49135400	Weak transcription	Fetal Heart	heart
34	chr3:49132600-49135400	Weak transcription	Stomach Mucosa	stomach
35	chr3:49132600-49135600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:49132800-49135000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:49132800-49135000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:49132800-49135400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr3:49132800-49135600	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:49132800-49136400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr3:49132800-49136400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:49133000-49135200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:49133000-49135400	Strong transcription	Spleen	Spleen
44	chr3:49133000-49136000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:49133000-49140000	Strong transcription	HSMMtube	muscle
46	chr3:49133000-49140200	Strong transcription	NHLF	lung
47	chr3:49133000-49140400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:49133000-49140400	Strong transcription	Right Ventricle	heart
49	chr3:49133000-49140600	Strong transcription	Fetal Muscle Leg	muscle
50	chr3:49133000-49140600	Strong transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links