Variant report

Variant	rs13197177
Chromosome Location	chr6:1890965-1890966
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10484693	0.84[CHB][hapmap];0.82[MEX][hapmap]
rs13190775	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13203536	1.00[CEU][hapmap]
rs13204935	0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs17772389	0.84[CHB][hapmap]
rs1998519	0.87[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35946812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778536	0.83[EUR][1000 genomes]
rs3800086	0.84[TSI][hapmap]
rs3800090	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs3800105	1.00[CHB][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs3823279	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57347378	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6596858	0.87[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs6912444	0.91[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs6927686	0.84[CHB][hapmap]
rs9503028	0.83[EUR][1000 genomes]
rs9503031	0.86[CHB][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs9503038	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
6	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
7	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
8	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
9	nsv883383	chr6:1775436-1918572	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv883384	chr6:1787862-1942538	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1032149	chr6:1848148-2006021	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv883385	chr6:1869592-1915828	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1851200-1895600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:1851400-1909600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:1871000-1895400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:1873800-1893000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:1877600-1915200	Weak transcription	Primary T cells from cord blood	blood
6	chr6:1886000-1896400	Weak transcription	Esophagus	oesophagus
7	chr6:1886200-1893200	Weak transcription	Gastric	stomach
8	chr6:1886200-1901400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:1886200-1904000	Weak transcription	Fetal Intestine Small	intestine
10	chr6:1886400-1893000	Weak transcription	HepG2	liver
11	chr6:1887000-1892400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:1889800-1893200	Weak transcription	Aorta	Aorta
13	chr6:1889800-1895400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:1890400-1891400	Enhancers	NHEK	skin
15	chr6:1890400-1895400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:1890600-1904000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:1890600-1911400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:1890800-1891000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:1890800-1891600	Enhancers	HMEC	breast

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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