Variant report

Variant	rs10826118
Chromosome Location	chr10:52262468-52262469
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52260554..52263861-chr10:52272806..52275340,3	K562	blood:
2	chr10:52261680..52263393-chr10:52269137..52270888,2	MCF-7	breast:
3	chr10:52261590..52264231-chr10:52382016..52385854,3	MCF-7	breast:
4	chr10:52260913..52263202-chr10:52364630..52366882,2	MCF-7	breast:
5	chr10:52260323..52263504-chr10:52265636..52267832,3	MCF-7	breast:
6	chr10:52230115..52234351-chr10:52258743..52262560,5	MCF-7	breast:
7	chr10:52230142..52232797-chr10:52261125..52263960,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction
ENSG00000230036	Chromatin interaction
ENSG00000225303	Chromatin interaction
ENSG00000226200	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1011881	0.81[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs10740714	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10763354	0.81[CHD][hapmap]
rs10763366	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs10763529	0.88[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10826100	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10826126	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11005937	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203377	0.83[ASN][1000 genomes]
rs1203413	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1203415	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12356922	0.83[EUR][1000 genomes]
rs1436211	0.82[CHD][hapmap]
rs1548256	0.88[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1569962	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1569963	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1810576	0.90[EUR][1000 genomes]
rs1916566	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2092996	0.88[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2099527	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2117958	0.82[ASN][1000 genomes]
rs2144862	0.88[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2339505	0.84[CEU][hapmap];0.91[JPT][hapmap];0.92[EUR][1000 genomes]
rs2339506	0.85[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs2574959	0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2688878	0.81[ASN][1000 genomes]
rs2842103	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2842111	0.82[ASN][1000 genomes]
rs2983346	0.85[AFR][1000 genomes]
rs4312019	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4536155	0.85[ASN][1000 genomes]
rs4935712	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]
rs4935727	0.88[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4935730	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7071603	0.88[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7075289	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7092014	0.82[ASN][1000 genomes]
rs715675	0.81[ASN][1000 genomes]
rs7904833	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs910818	0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs978588	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv895391	chr10:52260398-52291608	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52247000-52271200	Weak transcription	Colon Smooth Muscle	Colon
2	chr10:52249200-52266800	Weak transcription	Primary B cells from cord blood	blood
3	chr10:52253800-52268200	Weak transcription	Fetal Intestine Small	intestine
4	chr10:52255000-52267200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr10:52255400-52266600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr10:52256600-52263000	Weak transcription	Right Ventricle	heart
7	chr10:52258000-52266600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr10:52258000-52266600	Weak transcription	Ovary	ovary
9	chr10:52258000-52267200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr10:52258000-52271800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr10:52260400-52263600	Enhancers	Brain Substantia Nigra	brain
12	chr10:52260600-52264000	Enhancers	Brain Angular Gyrus	brain
13	chr10:52260600-52264000	Enhancers	HepG2	liver
14	chr10:52260800-52264400	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr10:52260800-52264600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr10:52260800-52264600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr10:52260800-52264600	Enhancers	Brain Cingulate Gyrus	brain
18	chr10:52261000-52268200	Weak transcription	Gastric	stomach
19	chr10:52261200-52264000	Enhancers	Brain Anterior Caudate	brain
20	chr10:52261400-52262800	Enhancers	K562	blood
21	chr10:52261400-52263800	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr10:52261400-52264000	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr10:52261400-52264400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr10:52261400-52266600	Weak transcription	Fetal Lung	lung
25	chr10:52261600-52262600	Enhancers	Fetal Intestine Large	intestine
26	chr10:52261600-52263600	Enhancers	Primary T cells fromperipheralblood	blood
27	chr10:52261600-52264200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr10:52261600-52264200	Enhancers	Fetal Heart	heart
29	chr10:52261600-52264400	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr10:52261600-52264600	Enhancers	Brain Hippocampus Middle	brain
31	chr10:52261800-52262600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr10:52261800-52262800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr10:52261800-52262800	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr10:52261800-52263600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr10:52261800-52263800	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr10:52261800-52263800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr10:52261800-52264000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr10:52261800-52264000	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr10:52261800-52264200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr10:52261800-52264600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr10:52261800-52266000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr10:52261800-52271400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr10:52262000-52262600	Enhancers	H9 Cell Line	embryonic stem cell
44	chr10:52262000-52262600	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr10:52262000-52262800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr10:52262000-52263000	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr10:52262000-52264000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr10:52262000-52266800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr10:52262000-52270800	Weak transcription	HSMMtube	muscle
50	chr10:52262200-52262600	Enhancers	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links