Variant report

Variant	rs3800121
Chromosome Location	chr6:1896681-1896682
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10900914	0.86[JPT][hapmap]
rs11969985	0.86[JPT][hapmap]
rs12664587	0.87[JPT][hapmap]
rs1467594	0.89[CEU][hapmap]
rs1543538	0.93[CEU][hapmap]
rs1570533	0.92[CEU][hapmap]
rs1570535	1.00[JPT][hapmap]
rs17134557	0.81[JPT][hapmap]
rs2281760	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2296131	0.96[CEU][hapmap]
rs2628442	0.87[JPT][hapmap]
rs2628445	0.86[JPT][hapmap]
rs2628455	0.81[JPT][hapmap]
rs2761233	0.86[JPT][hapmap]
rs3778537	0.85[CEU][hapmap]
rs3778540	0.89[CEU][hapmap]
rs3800091	0.89[CEU][hapmap]
rs3800097	0.89[CEU][hapmap];0.82[YRI][hapmap]
rs3800099	0.89[CEU][hapmap]
rs3800100	0.89[CEU][hapmap];0.82[YRI][hapmap]
rs3800102	0.88[CEU][hapmap]
rs3800103	0.89[CEU][hapmap]
rs3800104	0.89[CEU][hapmap]
rs3800107	0.85[CEU][hapmap]
rs3800115	1.00[CEU][hapmap];0.83[YRI][hapmap];0.90[EUR][1000 genomes]
rs3800122	0.92[CEU][hapmap]
rs3800136	0.86[JPT][hapmap]
rs3823277	0.89[CEU][hapmap]
rs4959160	1.00[JPT][hapmap]
rs6916130	0.81[JPT][hapmap]
rs6940806	0.88[CEU][hapmap]
rs7759192	0.86[JPT][hapmap]
rs7759496	0.87[JPT][hapmap]
rs912310	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9378661	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs9392341	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9392342	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs9405521	0.90[EUR][1000 genomes]
rs9405522	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]

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:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1851400-1909600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr6:1877600-1915200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:1886200-1901400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:1886200-1904000	Weak transcription	Fetal Intestine Small	intestine
5	chr6:1890600-1904000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:1890600-1911400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:1891800-1914800	Weak transcription	Colonic Mucosa	Colon
8	chr6:1893400-1897000	Weak transcription	HepG2	liver
9	chr6:1894200-1898200	Weak transcription	Gastric	stomach
10	chr6:1894200-1904000	Weak transcription	Pancreas	Pancrea
11	chr6:1895200-1897400	Enhancers	Stomach Mucosa	stomach
12	chr6:1895400-1897400	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr6:1895800-1904000	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:1895800-1910800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:1895800-1911200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:1896000-1916400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:1896200-1901400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:1896400-1897400	Enhancers	Esophagus	oesophagus
19	chr6:1896400-1901200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr6:1896400-1910800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:1896600-1899600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:1896600-1901400	Weak transcription	Aorta	Aorta
23	chr6:1896600-1901800	Weak transcription	Osteobl	bone
24	chr6:1896600-1904800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:1896600-1905000	Weak transcription	Duodenum Mucosa	Duodenum

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