Variant report

Variant	rs10490964
Chromosome Location	chr10:52256902-52256903
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52248823..52250649-chr10:52255298..52257622,2	MCF-7	breast:
2	chr10:52177672..52180517-chr10:52256358..52258147,2	MCF-7	breast:
3	chr10:52181046..52183288-chr10:52255236..52257097,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10490963	0.89[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11005626	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11005959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12257419	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12262259	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1369860	0.89[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs17438825	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17440448	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17518471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17519121	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17519380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17721658	0.89[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17721694	0.86[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17721713	1.00[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17778152	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1916568	0.89[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs1916569	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1916571	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2060560	0.85[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2064759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2117961	0.83[ASN][1000 genomes]
rs2117962	0.92[ASN][1000 genomes]
rs2255387	0.83[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs2255720	0.91[ASN][1000 genomes]
rs2255849	0.85[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2255853	0.84[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2255859	0.81[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2574955	0.85[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2574956	0.85[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2574981	0.91[ASN][1000 genomes]
rs2688875	0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs2688877	0.85[ASN][1000 genomes]
rs2688879	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2842102	0.91[ASN][1000 genomes]
rs2842105	0.91[ASN][1000 genomes]
rs2842106	0.91[ASN][1000 genomes]
rs2842107	0.85[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2842109	0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs34672995	0.89[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34928652	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802537	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4935152	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4935673	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4935703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4935713	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4935729	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4935731	0.90[AMR][1000 genomes]
rs4935732	0.90[AMR][1000 genomes]
rs55773344	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55861418	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56078228	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56080689	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56133398	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56225400	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56268559	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56277433	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56403030	0.90[AMR][1000 genomes]
rs61559519	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61741330	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61856761	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61856763	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61856778	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61856782	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61856787	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61856788	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61856793	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61856794	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61856795	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61856828	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61856832	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61858062	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61858064	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61858065	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61858068	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61858069	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61858108	0.89[AMR][1000 genomes]
rs61858206	0.92[ASN][1000 genomes]
rs61858207	0.92[ASN][1000 genomes]
rs7067626	0.89[CEU][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7068430	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];0.80[MKK][hapmap];0.94[TSI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7069115	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7082805	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7092753	0.98[ASN][1000 genomes]
rs7099450	0.81[CEU][hapmap];0.87[TSI][hapmap]
rs72801752	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72801754	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72801768	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72801775	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72801776	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72801781	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7392702	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7475420	0.86[ASN][1000 genomes]
rs7921632	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs884880	1.00[ASW][hapmap];0.89[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.92[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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52231200-52257800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr10:52234000-52261600	Weak transcription	Pancreas	Pancrea
3	chr10:52237800-52261800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr10:52244400-52261800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr10:52244800-52261800	Weak transcription	Primary T cells from cord blood	blood
6	chr10:52244800-52262000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr10:52247000-52271200	Weak transcription	Colon Smooth Muscle	Colon
8	chr10:52248000-52261800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr10:52248800-52257600	Weak transcription	Ovary	ovary
10	chr10:52249200-52266800	Weak transcription	Primary B cells from cord blood	blood
11	chr10:52253800-52268200	Weak transcription	Fetal Intestine Small	intestine
12	chr10:52255000-52257200	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr10:52255000-52267200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr10:52255200-52257800	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr10:52255400-52258000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr10:52255400-52266600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr10:52255600-52257200	Enhancers	Brain Cingulate Gyrus	brain
18	chr10:52255600-52257200	Flanking Active TSS	GM12878-XiMat	blood
19	chr10:52255600-52257400	Enhancers	Brain Hippocampus Middle	brain
20	chr10:52255800-52257000	Enhancers	Brain Anterior Caudate	brain
21	chr10:52255800-52257000	Enhancers	Right Atrium	heart
22	chr10:52256000-52257400	Enhancers	Brain Angular Gyrus	brain
23	chr10:52256200-52257600	Enhancers	Left Ventricle	heart
24	chr10:52256200-52257600	Weak transcription	K562	blood
25	chr10:52256400-52258000	Enhancers	Fetal Heart	heart
26	chr10:52256400-52261400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr10:52256400-52261800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr10:52256600-52257400	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr10:52256600-52258000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr10:52256600-52263000	Weak transcription	Right Ventricle	heart
31	chr10:52256800-52257000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr10:52256800-52257200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr10:52256800-52257600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr10:52256800-52260400	Weak transcription	Brain Substantia Nigra	brain

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