Variant report

Variant	rs11005959
Chromosome Location	chr10:52262733-52262734
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	chr10:52230142..52232797-chr10:52261125..52263960,2	MCF-7	breast:

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

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10490963	0.89[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10490964	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]
rs11005626	0.93[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11005832	0.81[YRI][hapmap]
rs12246361	0.81[YRI][hapmap]
rs12257419	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12262259	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12264817	0.81[YRI][hapmap]
rs1369860	0.89[CEU][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs17438825	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17440448	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[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];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17519121	0.95[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];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17721658	0.89[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17721694	0.86[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17721713	0.89[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17778152	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1916568	0.89[CEU][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];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1916571	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2060560	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];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2117961	0.83[ASN][1000 genomes]
rs2117962	0.92[ASN][1000 genomes]
rs2255387	0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs2255720	0.91[ASN][1000 genomes]
rs2255849	0.96[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2255853	0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2255859	0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2574955	0.96[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2574956	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	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	0.96[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];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34928652	0.95[AMR][1000 genomes];0.96[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];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4935152	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4935673	0.82[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];0.88[MKK][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4935713	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4935729	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4935731	0.80[AMR][1000 genomes]
rs4935732	0.80[AMR][1000 genomes]
rs55773344	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55861418	0.83[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	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56133398	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56225400	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56268559	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56277433	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56403030	0.80[AMR][1000 genomes]
rs61559519	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61741330	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61856761	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61856763	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61856778	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61856782	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61856787	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61856788	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61856793	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61856794	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61856795	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61856828	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61856832	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61858062	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61858064	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61858065	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61858068	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61858069	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61858206	0.92[ASN][1000 genomes]
rs61858207	0.92[ASN][1000 genomes]
rs7067626	0.89[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7068430	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];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7069115	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7082805	0.83[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	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72801768	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72801775	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72801776	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72801781	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7392702	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7475420	0.86[ASN][1000 genomes]
rs7921632	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs884880	0.89[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.92[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	chr10:52261600-52263600	Enhancers	Primary T cells fromperipheralblood	blood
26	chr10:52261600-52264200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr10:52261600-52264200	Enhancers	Fetal Heart	heart
28	chr10:52261600-52264400	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr10:52261600-52264600	Enhancers	Brain Hippocampus Middle	brain
30	chr10:52261800-52262800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr10:52261800-52262800	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr10:52261800-52263600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr10:52261800-52263800	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr10:52261800-52263800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr10:52261800-52264000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr10:52261800-52264000	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr10:52261800-52264200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr10:52261800-52264600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr10:52261800-52266000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr10:52261800-52271400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr10:52262000-52262800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr10:52262000-52263000	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr10:52262000-52264000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr10:52262000-52266800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr10:52262000-52270800	Weak transcription	HSMMtube	muscle
46	chr10:52262200-52262800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr10:52262200-52263200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr10:52262200-52263600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr10:52262200-52265400	Weak transcription	Pancreas	Pancrea
50	chr10:52262200-52266200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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