Variant report

Variant	rs6691170
Chromosome Location	chr1:222045446-222045447
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222042910..222045685-chr1:222046384..222048524,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10746414	1.00[CHD][hapmap]
rs10863657	1.00[ASN][1000 genomes]
rs10863664	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11118874	1.00[ASN][1000 genomes]
rs11118875	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11579490	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582814	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	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125690	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12130910	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35090621	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4308986	0.81[EUR][1000 genomes]
rs4384245	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4528124	0.86[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs4581289	1.00[ASN][1000 genomes]
rs56010022	1.00[ASN][1000 genomes]
rs6604675	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6604676	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6604677	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604678	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658977	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659311	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668784	1.00[ASN][1000 genomes]
rs66698149	1.00[ASN][1000 genomes]
rs6699132	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67087803	1.00[ASN][1000 genomes]
rs67220535	1.00[ASN][1000 genomes]
rs7515604	1.00[CHB][hapmap]
rs7544478	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7544656	1.00[CHB][hapmap]
rs7550628	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556214	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556228	0.87[AMR][1000 genomes];0.97[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

Variant related diseases (count:1)

Disease	PMID	Source
Colorectal cancer	20972440	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6691170	AIDA	cis	parietal	SCAN
rs6691170	HHIPL2	cis	cerebellum	SCAN

Chromatin state (count:18 , 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	chr1:222043200-222052800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:222043400-222047200	Weak transcription	HSMM	muscle
5	chr1:222043400-222047200	Weak transcription	NH-A	brain
6	chr1:222043400-222047400	Weak transcription	HMEC	breast
7	chr1:222043400-222051400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:222043400-222052600	Weak transcription	HSMMtube	muscle
9	chr1:222043600-222047200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:222043600-222047200	Weak transcription	Osteobl	bone
11	chr1:222043800-222046800	Weak transcription	NHLF	lung
12	chr1:222043800-222047200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:222043800-222047200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:222044400-222045800	Weak transcription	NHDF-Ad	bronchial
15	chr1:222044400-222046000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:222044400-222047000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:222044400-222047000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:222044400-222047200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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