Variant report

Variant	rs6604677
Chromosome Location	chr1:222042217-222042218
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:222002904..222005869-chr1:222041266..222043979,2	MCF-7	breast:
2	chr1:221912612..221914842-chr1:222041850..222044308,2	MCF-7	breast:
3	chr1:222039489..222042458-chr1:222046746..222048738,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10746414	1.00[CHB][hapmap]
rs10863657	1.00[ASN][1000 genomes]
rs10863664	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11118874	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118875	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11118883	1.00[CHB][hapmap]
rs11577023	1.00[CHB][hapmap]
rs11579490	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582814	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12083393	1.00[ASN][1000 genomes]
rs12089785	1.00[ASN][1000 genomes]
rs12090948	1.00[ASN][1000 genomes]
rs12095068	1.00[ASN][1000 genomes]
rs12118052	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125690	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12130910	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35090621	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4308986	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs4384245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4528124	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs4581289	1.00[ASN][1000 genomes]
rs56010022	1.00[ASN][1000 genomes]
rs6604675	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6604676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6604678	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658977	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659311	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668784	1.00[ASN][1000 genomes]
rs66698149	1.00[ASN][1000 genomes]
rs6691170	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699132	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67087803	1.00[ASN][1000 genomes]
rs67220535	1.00[ASN][1000 genomes]
rs7544478	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7550628	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556214	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556228	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222019800-222047600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:222040800-222049800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:222041400-222043400	Enhancers	HMEC	breast
4	chr1:222041400-222044400	Enhancers	NHDF-Ad	bronchial
5	chr1:222041600-222043400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:222041600-222043400	Enhancers	Hela-S3	cervix
7	chr1:222041600-222043400	Enhancers	NH-A	brain
8	chr1:222041600-222043400	Enhancers	NHEK	skin
9	chr1:222041600-222043600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:222041600-222043800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:222041600-222043800	Enhancers	NHLF	lung
12	chr1:222041600-222044400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:222041600-222044400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:222041800-222043000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:222041800-222043000	Enhancers	HUVEC	blood vessel
16	chr1:222041800-222043400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:222041800-222043400	Enhancers	HSMM	muscle
18	chr1:222041800-222043600	Enhancers	Osteobl	bone
19	chr1:222042000-222042400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:222042000-222042800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:222042000-222043200	Enhancers	Stomach Mucosa	stomach
22	chr1:222042200-222042400	Flanking Active TSS	A549	lung
23	chr1:222042200-222043800	Enhancers	Muscle Satellite Cultured Cells	--
24	chr1:222042200-222043800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links