Variant report

Variant	rs12407319
Chromosome Location	chr1:152365929-152365930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:152358713..152362980-chr1:152363568..152366676,4	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10788835	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10888486	0.85[CEU][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs11204982	0.93[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11204984	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204985	0.93[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11204986	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11204987	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11204995	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204998	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11301808	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11588022	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11803108	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12022217	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12027445	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12029431	0.81[JPT][hapmap]
rs12029633	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12032854	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12049036	0.85[JPT][hapmap]
rs12402680	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12403031	0.93[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12408401	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12568784	0.93[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1858485	0.93[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1923493	0.86[JPT][hapmap]
rs1923505	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1923506	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1923509	0.80[AMR][1000 genomes]
rs1933066	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2065954	0.93[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2146119	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2275264	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2282303	0.93[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2525	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3120665	0.93[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3120666	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3120667	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3126099	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3753443	0.86[JPT][hapmap];0.89[MEX][hapmap]
rs3753444	0.86[JPT][hapmap]
rs3818831	0.93[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3829868	0.85[JPT][hapmap];0.89[MEX][hapmap]
rs4285700	0.86[JPT][hapmap];0.89[MEX][hapmap]
rs4378206	0.93[CEU][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs45541239	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6587668	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6679449	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs6693160	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7514696	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7515448	0.93[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7521839	0.86[JPT][hapmap]
rs941935	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9633410	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1005472	chr1:152247763-152443448	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv535161	chr1:152247763-152443448	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv916016	chr1:152337775-152590520	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12407319	S100A7A	cis	parietal	SCAN
rs12407319	AQP10	cis	parietal	SCAN
rs12407319	IVL	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152363800-152368000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr1:152363800-152368200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:152363800-152368200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:152364000-152366600	Enhancers	NHEK	skin
5	chr1:152364600-152366400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:152364800-152366200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:152364800-152366800	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr1:152365000-152366000	Bivalent Enhancer	HMEC	breast
9	chr1:152365800-152366200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:152365800-152367000	Enhancers	Primary T helper cells fromperipheralblood	blood

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