Variant report

Variant	rs3800053
Chromosome Location	chr6:1773865-1773866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:1640395..1643139-chr6:1772426..1774181,2	MCF-7	breast:
2	chr6:1772266..1774519-chr6:1779951..1781505,2	K562	blood:
3	chr6:1773332..1775371-chr6:1778272..1781076,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1040532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016052	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2318089	0.87[JPT][hapmap]
rs3778519	0.83[JPT][hapmap]
rs3800058	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs722585	0.82[JPT][hapmap]
rs722587	0.86[JPT][hapmap]
rs7745811	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7745817	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7760202	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7760204	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1020603	chr6:1697548-1921374	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv538093	chr6:1697548-1921374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv600809	chr6:1732741-1775436	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv538094	chr6:1757776-1907505	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1749800-1779000	Weak transcription	Aorta	Aorta
2	chr6:1751200-1780400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:1762800-1801600	Weak transcription	Colonic Mucosa	Colon
4	chr6:1763000-1792600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:1768000-1778400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:1768000-1778600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:1768200-1775200	Weak transcription	Psoas Muscle	Psoas
8	chr6:1768200-1777000	Weak transcription	Left Ventricle	heart
9	chr6:1768200-1778400	Weak transcription	Brain Anterior Caudate	brain
10	chr6:1768200-1803600	Weak transcription	Small Intestine	intestine
11	chr6:1768600-1778200	Weak transcription	Fetal Kidney	kidney
12	chr6:1768800-1779400	Weak transcription	Hela-S3	cervix
13	chr6:1770200-1776000	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr6:1770600-1774200	Strong transcription	HepG2	liver
15	chr6:1770800-1774400	Weak transcription	Fetal Muscle Leg	muscle
16	chr6:1770800-1775000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr6:1770800-1792600	Weak transcription	Thymus	Thymus
18	chr6:1770800-1805600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:1771000-1774000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:1771000-1774200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr6:1771000-1776000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr6:1771200-1776200	Enhancers	Primary T cells from cord blood	blood
23	chr6:1771800-1785600	Weak transcription	Pancreas	Pancrea
24	chr6:1772000-1774400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:1772000-1774400	Weak transcription	NHLF	lung
26	chr6:1772000-1774600	Weak transcription	Fetal Stomach	stomach
27	chr6:1772000-1774600	Weak transcription	NHDF-Ad	bronchial
28	chr6:1772000-1788400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:1772000-1798800	Weak transcription	Gastric	stomach
30	chr6:1772200-1774000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:1772200-1774400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:1772200-1774800	Weak transcription	NH-A	brain
33	chr6:1772200-1788000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:1772400-1774800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:1773000-1774600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:1773000-1775000	Enhancers	Fetal Lung	lung
37	chr6:1773200-1775000	Enhancers	Fetal Intestine Large	intestine
38	chr6:1773600-1774000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:1773600-1774000	Enhancers	Fetal Thymus	thymus
40	chr6:1773600-1774600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:1773600-1774600	Enhancers	Primary T cells fromperipheralblood	blood
42	chr6:1773600-1774600	Enhancers	Duodenum Mucosa	Duodenum
43	chr6:1773600-1774600	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr6:1773600-1774800	Enhancers	Fetal Intestine Small	intestine
45	chr6:1773600-1775000	Enhancers	Primary hematopoietic stem cells	blood
46	chr6:1773600-1775000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:1773600-1775200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:1773600-1775200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr6:1773800-1774400	Enhancers	GM12878-XiMat	blood
50	chr6:1773800-1774800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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