Variant report

Variant	rs12262002
Chromosome Location	chr10:52258524-52258525
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:52231577..52234043-chr10:52257070..52259617,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225303	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10159614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10825837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10825903	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11005454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11005901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005920	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006017	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11814231	1.00[YRI][hapmap]
rs11815109	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12244472	1.00[AMR][1000 genomes]
rs12245522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12246357	1.00[AMR][1000 genomes]
rs12251096	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12251514	0.93[EUR][1000 genomes]
rs12253726	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12253887	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12255967	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12262586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12265260	0.82[ASN][1000 genomes]
rs12265364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011793	1.00[YRI][hapmap]
rs61152656	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7077375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7097717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7097865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73316672	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73316673	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73316690	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73316698	0.81[AFR][1000 genomes]
rs73332908	1.00[AMR][1000 genomes]
rs73332909	1.00[AMR][1000 genomes]
rs7358033	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7916018	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7922659	1.00[YRI][hapmap]

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:48 , 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	chr10:52258000-52259000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr10:52258000-52260600	Weak transcription	Brain Angular Gyrus	brain
24	chr10:52258000-52260600	Weak transcription	Brain Hippocampus Middle	brain
25	chr10:52258000-52260600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr10:52258000-52260600	Weak transcription	HepG2	liver
27	chr10:52258000-52260800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr10:52258000-52260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr10:52258000-52260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr10:52258000-52260800	Weak transcription	NHEK	skin
31	chr10:52258000-52261000	Weak transcription	NHLF	lung
32	chr10:52258000-52261400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr10:52258000-52261400	Weak transcription	HSMMtube	muscle
34	chr10:52258000-52261600	Weak transcription	Fetal Heart	heart
35	chr10:52258000-52261600	Weak transcription	Hela-S3	cervix
36	chr10:52258000-52261800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr10:52258000-52261800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr10:52258000-52266600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr10:52258000-52266600	Weak transcription	Ovary	ovary
40	chr10:52258000-52267200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr10:52258000-52271800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr10:52258200-52261400	Weak transcription	HSMM	muscle
43	chr10:52258200-52261400	Weak transcription	K562	blood
44	chr10:52258200-52261600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr10:52258400-52258600	Flanking Active TSS	GM12878-XiMat	blood
46	chr10:52258400-52261000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr10:52258400-52261200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr10:52258400-52261400	Weak transcription	Osteobl	bone

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