Variant report

Variant	rs4140588
Chromosome Location	chr6:1740933-1740934
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1013303	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1040530	0.81[JPT][hapmap]
rs12200248	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs12529650	0.85[JPT][hapmap]
rs3734739	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3734740	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs3800032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3800034	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3800035	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs3800036	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs3800037	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs3800038	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3800040	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3800043	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs3823262	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4546532	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4959605	0.81[JPT][hapmap]
rs6914704	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs6933551	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs742536	0.89[CEU][hapmap]
rs761148	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs9392332	0.82[CHB][hapmap];0.81[JPT][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	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

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1701200-1749400	Weak transcription	Colonic Mucosa	Colon
2	chr6:1716000-1749200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:1721200-1746200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:1721200-1748800	Weak transcription	Osteobl	bone
5	chr6:1723000-1743200	Strong transcription	HepG2	liver
6	chr6:1726800-1749000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:1726800-1749000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:1731800-1745000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:1731800-1746200	Weak transcription	Right Atrium	heart
10	chr6:1732200-1744800	Weak transcription	Aorta	Aorta
11	chr6:1732200-1750600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:1732200-1756600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:1735800-1741600	Weak transcription	Fetal Intestine Small	intestine
14	chr6:1736000-1746200	Weak transcription	Esophagus	oesophagus
15	chr6:1736000-1746200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:1736400-1746200	Weak transcription	Right Ventricle	heart
17	chr6:1737000-1749000	Weak transcription	Stomach Mucosa	stomach
18	chr6:1737400-1746200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:1738000-1741000	Enhancers	Primary B cells from peripheral blood	blood
20	chr6:1738400-1744800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:1738400-1744800	Weak transcription	Pancreas	Pancrea
22	chr6:1738400-1745800	Weak transcription	Fetal Kidney	kidney
23	chr6:1738400-1746200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:1738400-1762400	Weak transcription	Gastric	stomach
25	chr6:1738400-1768200	Weak transcription	Primary T cells from cord blood	blood
26	chr6:1739400-1746000	Weak transcription	HUVEC	blood vessel
27	chr6:1739600-1746000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr6:1740000-1741600	Enhancers	GM12878-XiMat	blood
29	chr6:1740000-1744800	Weak transcription	Spleen	Spleen

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