Variant report

Variant	rs857147
Chromosome Location	chr1:57177789-57177790
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10789038	0.89[CEU][hapmap]
rs10889008	0.85[CEU][hapmap]
rs10889010	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11206889	0.81[CEU][hapmap];0.85[MEX][hapmap]
rs11206890	0.85[CEU][hapmap]
rs11206899	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11206900	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1124900	0.92[CEU][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs12070903	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2064421	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2064422	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2092594	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2092595	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2143754	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2245475	0.82[EUR][1000 genomes]
rs2746338	0.92[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2746339	0.92[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2746348	0.88[CEU][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes]
rs2746349	0.92[CEU][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs2796491	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2796492	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2796493	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2796495	0.92[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2796496	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2796498	0.92[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2796499	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2796506	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2796507	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2796509	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2796511	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2796512	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2796514	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2796519	0.85[CEU][hapmap]
rs2796534	0.84[CEU][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2796541	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6588643	0.83[EUR][1000 genomes]
rs6671760	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6683935	0.83[EUR][1000 genomes]
rs715404	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs715405	0.92[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7366969	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7367181	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7367199	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7415042	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7419053	0.82[CEU][hapmap]
rs7515414	0.82[CEU][hapmap]
rs857132	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs857148	0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs857150	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs857155	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs857156	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs857159	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs932447	0.81[CEU][hapmap]
rs963528	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv523032	chr1:57116909-57249558	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv520726	chr1:57143986-57205666	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs857147	C1orf175	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57166200-57178800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:57170000-57181200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:57170200-57185000	Weak transcription	Liver	Liver
4	chr1:57173400-57181400	Weak transcription	Left Ventricle	heart
5	chr1:57173400-57184200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:57175200-57178000	Enhancers	NH-A	brain
7	chr1:57175400-57178000	Enhancers	NHLF	lung
8	chr1:57175800-57178000	Enhancers	NHDF-Ad	bronchial
9	chr1:57175800-57178200	Enhancers	Osteobl	bone
10	chr1:57176000-57178000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr1:57176200-57178400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:57176200-57184000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:57176800-57180800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:57177000-57178000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:57177000-57178600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:57177000-57185000	Weak transcription	Fetal Heart	heart
17	chr1:57177200-57180800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:57177200-57180800	Weak transcription	NHEK	skin
19	chr1:57177200-57181000	Weak transcription	HSMM	muscle
20	chr1:57177200-57181200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:57177400-57180600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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