Variant report

Variant	rs4935712
Chromosome Location	chr10:52259413-52259414
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52231577..52234043-chr10:52257070..52259617,2	MCF-7	breast:
2	chr10:52230115..52234351-chr10:52258743..52262560,5	MCF-7	breast:
3	chr10:52259203..52261063-chr10:52265716..52267291,2	K562	blood:

Variant related genes	Relation type
ENSG00000225303	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1011881	0.88[CEU][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10740714	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10763354	0.81[CHD][hapmap]
rs10763366	0.82[CHB][hapmap]
rs10763529	0.88[CEU][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10826100	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10826118	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10826126	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11005937	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203377	0.82[ASN][1000 genomes]
rs1203413	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1203415	0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12356922	0.84[EUR][1000 genomes]
rs1436211	0.82[CHD][hapmap]
rs1548256	0.88[CEU][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1569962	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1569963	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1810576	0.91[EUR][1000 genomes]
rs1916566	0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2092996	0.88[CEU][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2099527	0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2117958	0.81[ASN][1000 genomes]
rs2144862	0.88[CEU][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2339505	0.92[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2339506	0.90[CEU][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2574959	0.82[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2842103	0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2842111	0.81[ASN][1000 genomes]
rs4312019	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4536155	0.83[ASN][1000 genomes]
rs4935727	0.88[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4935730	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7071603	0.88[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7075289	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7092014	0.81[ASN][1000 genomes]
rs715675	0.80[ASN][1000 genomes]
rs7904833	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs978588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52234000-52261600	Weak transcription	Pancreas	Pancrea
2	chr10:52237800-52261800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr10:52244400-52261800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr10:52244800-52261800	Weak transcription	Primary T cells from cord blood	blood
5	chr10:52244800-52262000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr10:52247000-52271200	Weak transcription	Colon Smooth Muscle	Colon
7	chr10:52248000-52261800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr10:52249200-52266800	Weak transcription	Primary B cells from cord blood	blood
9	chr10:52253800-52268200	Weak transcription	Fetal Intestine Small	intestine
10	chr10:52255000-52267200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr10:52255400-52266600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr10:52256400-52261400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr10:52256400-52261800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr10:52256600-52263000	Weak transcription	Right Ventricle	heart
15	chr10:52256800-52260400	Weak transcription	Brain Substantia Nigra	brain
16	chr10:52257000-52261200	Weak transcription	Brain Anterior Caudate	brain
17	chr10:52257000-52261800	Weak transcription	Right Atrium	heart
18	chr10:52257200-52260800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr10:52257200-52260800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr10:52257600-52261800	Weak transcription	Left Ventricle	heart
21	chr10:52257800-52260800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr10:52258000-52260600	Weak transcription	Brain Angular Gyrus	brain
23	chr10:52258000-52260600	Weak transcription	Brain Hippocampus Middle	brain
24	chr10:52258000-52260600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr10:52258000-52260600	Weak transcription	HepG2	liver
26	chr10:52258000-52260800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr10:52258000-52260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr10:52258000-52260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr10:52258000-52260800	Weak transcription	NHEK	skin
30	chr10:52258000-52261000	Weak transcription	NHLF	lung
31	chr10:52258000-52261400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr10:52258000-52261400	Weak transcription	HSMMtube	muscle
33	chr10:52258000-52261600	Weak transcription	Fetal Heart	heart
34	chr10:52258000-52261600	Weak transcription	Hela-S3	cervix
35	chr10:52258000-52261800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr10:52258000-52261800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr10:52258000-52266600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr10:52258000-52266600	Weak transcription	Ovary	ovary
39	chr10:52258000-52267200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr10:52258000-52271800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr10:52258200-52261400	Weak transcription	HSMM	muscle
42	chr10:52258200-52261400	Weak transcription	K562	blood
43	chr10:52258200-52261600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr10:52258400-52261000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr10:52258400-52261200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr10:52258400-52261400	Weak transcription	Osteobl	bone
47	chr10:52259200-52261600	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links