Variant report

Variant	rs3800040
Chromosome Location	chr6:1763048-1763049
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:1762522..1764369-chr6:1837443..1839225,2	MCF-7	breast:
2	chr6:1762365..1765398-chr6:1767554..1769715,3	K562	blood:
3	chr6:1616799..1619206-chr6:1761673..1763182,2	MCF-7	breast:
4	chr6:1606384..1611793-chr6:1762059..1766159,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054598	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1013303	0.81[JPT][hapmap]
rs1040530	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs10458130	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12200248	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs12208162	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12529650	0.85[JPT][hapmap]
rs34669469	0.92[ASN][1000 genomes]
rs3734739	0.81[JPT][hapmap]
rs3734740	0.81[JPT][hapmap]
rs3800032	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3800034	0.81[JPT][hapmap]
rs3800035	0.81[JPT][hapmap]
rs3800036	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes]
rs3800037	0.92[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs3800038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3800043	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs3823262	0.81[JPT][hapmap]
rs4140588	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4546532	0.81[JPT][hapmap]
rs4959605	0.81[JPT][hapmap]
rs56046637	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62388352	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6596850	0.96[EUR][1000 genomes]
rs6912189	0.94[EUR][1000 genomes]
rs6914704	0.92[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs6916153	0.88[EUR][1000 genomes]
rs6920971	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6933551	0.81[JPT][hapmap]
rs742536	0.92[CEU][hapmap]
rs761148	0.81[JPT][hapmap]
rs9392332	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1738400-1768200	Weak transcription	Primary T cells from cord blood	blood
2	chr6:1749800-1779000	Weak transcription	Aorta	Aorta
3	chr6:1751200-1780400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr6:1757000-1766000	Weak transcription	Right Atrium	heart
5	chr6:1757200-1764000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:1757200-1766800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:1757200-1770600	Weak transcription	Lung	lung
8	chr6:1758600-1771400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr6:1758800-1767800	Weak transcription	Small Intestine	intestine
10	chr6:1760800-1763200	Enhancers	Brain Germinal Matrix	brain
11	chr6:1761000-1768400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:1761200-1764200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:1761600-1763600	Enhancers	Stomach Mucosa	stomach
14	chr6:1761600-1763800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr6:1761600-1767400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:1761800-1764200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:1762200-1763200	Enhancers	Duodenum Mucosa	Duodenum
18	chr6:1762200-1765000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:1762400-1763200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:1762400-1764200	Enhancers	NHEK	skin
21	chr6:1762600-1764000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr6:1762600-1767800	Weak transcription	Brain Substantia Nigra	brain
23	chr6:1762600-1770600	Weak transcription	Brain Hippocampus Middle	brain
24	chr6:1762800-1763600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:1762800-1763600	Genic enhancers	HepG2	liver
26	chr6:1762800-1764400	Enhancers	Pancreas	Pancrea
27	chr6:1762800-1767800	Weak transcription	Fetal Intestine Large	intestine
28	chr6:1762800-1801600	Weak transcription	Colonic Mucosa	Colon
29	chr6:1763000-1763600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:1763000-1764000	Weak transcription	Fetal Lung	lung
31	chr6:1763000-1764200	Weak transcription	Fetal Kidney	kidney
32	chr6:1763000-1764200	Enhancers	HMEC	breast
33	chr6:1763000-1765800	Weak transcription	Fetal Intestine Small	intestine
34	chr6:1763000-1766200	Weak transcription	Gastric	stomach
35	chr6:1763000-1767000	Weak transcription	Osteobl	bone
36	chr6:1763000-1792600	Weak transcription	Rectal Mucosa Donor 29	rectum

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