Variant report

Variant	rs13062576
Chromosome Location	chr3:48536615-48536616
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48509136..48510838-chr3:48536578..48538592,2	MCF-7	breast:
2	chr3:48504031..48516338-chr3:48532689..48546353,31	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164054	Chromatin interaction
ENSG00000213689	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10049154	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10470687	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs13060933	1.00[CEU][hapmap]
rs13063312	0.82[CHB][hapmap]
rs13064619	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13091944	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs13094578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13100178	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13324142	0.82[CHB][hapmap]
rs1459246	1.00[CEU][hapmap]
rs1459247	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1870441	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2006871	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs2276850	0.82[CHB][hapmap]
rs2854394	1.00[CEU][hapmap]
rs28563843	0.84[ASN][1000 genomes]
rs28881595	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3806694	1.00[CHB][hapmap]
rs3821876	0.82[CHB][hapmap]
rs3969942	0.82[CHB][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4075082	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442126	1.00[CHB][hapmap]
rs6442127	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6765317	0.91[ASN][1000 genomes]
rs6781283	1.00[CEU][hapmap]
rs6785845	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6786424	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6792525	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs6806059	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6809981	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs734071	0.95[YRI][hapmap]
rs7428949	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7434077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7434107	0.97[ASN][1000 genomes]
rs7623614	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7640031	0.97[ASN][1000 genomes]
rs7644771	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs876597	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9810549	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs9810991	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs9816942	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9822677	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9835827	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9835902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9837687	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs9848824	0.84[ASN][1000 genomes]
rs9849280	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9850102	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9851743	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9851771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9864729	0.84[ASN][1000 genomes]
rs986739	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs986740	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs986742	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9869698	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs9871180	1.00[CEU][hapmap]
rs9871608	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9875911	1.00[CHB][hapmap]
rs9882962	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[EUR][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	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv1802114	chr3:48498822-48577670	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48514800-48541000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:48515000-48537400	Weak transcription	NHLF	lung
3	chr3:48515000-48539600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:48515000-48539800	Weak transcription	Osteobl	bone
5	chr3:48515000-48540200	Weak transcription	NHDF-Ad	bronchial
6	chr3:48515000-48540400	Weak transcription	HSMM	muscle
7	chr3:48515000-48541000	Weak transcription	Aorta	Aorta
8	chr3:48515200-48537400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:48515200-48538600	Weak transcription	Small Intestine	intestine
10	chr3:48515200-48539800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:48515200-48540000	Weak transcription	Brain Angular Gyrus	brain
12	chr3:48515200-48540200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:48515200-48540200	Weak transcription	HUVEC	blood vessel
14	chr3:48515200-48540400	Weak transcription	Fetal Brain Female	brain
15	chr3:48515200-48540600	Weak transcription	Brain Germinal Matrix	brain
16	chr3:48515200-48540600	Weak transcription	Fetal Lung	lung
17	chr3:48515400-48538200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:48517200-48537400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:48517200-48540400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:48517200-48540400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:48519600-48538600	Weak transcription	Right Atrium	heart
22	chr3:48519600-48540200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:48519800-48539600	Weak transcription	Right Ventricle	heart
24	chr3:48520600-48538200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:48520800-48537400	Weak transcription	Gastric	stomach
26	chr3:48520800-48537600	Weak transcription	Spleen	Spleen
27	chr3:48520800-48540000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr3:48522200-48539800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:48522400-48538400	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr3:48522400-48539000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr3:48526600-48540200	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:48527200-48539600	Weak transcription	Left Ventricle	heart
33	chr3:48530600-48540000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr3:48530800-48540400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr3:48531000-48540600	Weak transcription	A549	lung
36	chr3:48531400-48539000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr3:48531800-48539600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:48532200-48540200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:48532400-48540200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:48532600-48539000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:48533000-48540000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:48533200-48541200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:48533400-48538000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:48533400-48538000	Weak transcription	HMEC	breast
45	chr3:48533400-48538000	Weak transcription	NHEK	skin
46	chr3:48533400-48540200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:48533400-48540600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr3:48533600-48539000	Strong transcription	Fetal Intestine Small	intestine
49	chr3:48533600-48539600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:48533800-48537000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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