Variant report

Variant	rs12890123
Chromosome Location	chr14:65998069-65998070
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	chr14:65996757..65998904-chr14:66010555..66012729,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10483780	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11158596	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11158601	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11158602	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11620749	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11621680	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11622014	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11624045	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11627084	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11627184	0.82[EUR][1000 genomes]
rs11627185	0.82[EUR][1000 genomes]
rs11628196	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11851576	0.81[ASN][1000 genomes]
rs12589698	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12879202	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12879805	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12879971	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12883815	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12886334	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12887134	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12889002	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12890902	0.85[EUR][1000 genomes]
rs12890978	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12892058	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12895074	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12896663	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1953416	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1958561	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1998036	0.80[ASN][1000 genomes]
rs2002692	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2064694	0.80[EUR][1000 genomes]
rs2149841	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2184603	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2268961	0.80[EUR][1000 genomes]
rs2268962	0.80[EUR][1000 genomes]
rs2300865	0.83[EUR][1000 genomes]
rs2411355	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2411357	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2411816	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2411822	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3783709	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3825640	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4456409	0.84[EUR][1000 genomes]
rs4581615	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4899179	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4902400	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4902407	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67957534	0.82[EUR][1000 genomes]
rs7142651	0.81[EUR][1000 genomes]
rs7146742	0.91[ASN][1000 genomes]
rs7153297	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7154536	0.96[ASN][1000 genomes]
rs7155541	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7161123	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs743085	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7493004	0.82[EUR][1000 genomes]
rs8005710	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8012278	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs867972	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs883081	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs883082	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9796385	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036403	chr14:65724229-66208114	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv1043943	chr14:65782466-66698411	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
3	nsv542120	chr14:65782466-66698411	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
4	nsv1039168	chr14:65811750-66308343	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
5	esv3366524	chr14:65924360-66423862	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv456327	chr14:65955517-66052901	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv564951	chr14:65955517-66052901	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv832819	chr14:65957949-66106019	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65984800-66003000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr14:65985000-66025200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr14:65995200-66028000	Weak transcription	Dnd41	blood
4	chr14:65995400-65998400	Weak transcription	Brain Hippocampus Middle	brain
5	chr14:65995400-65998400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr14:65995400-65998800	Weak transcription	Ovary	ovary
7	chr14:65995400-66004600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr14:65995400-66004600	Weak transcription	Pancreas	Pancrea
9	chr14:65995400-66004600	Weak transcription	Thymus	Thymus
10	chr14:65995400-66006600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr14:65995400-66061000	Weak transcription	Gastric	stomach
12	chr14:65996000-65999000	Enhancers	Primary B cells from peripheral blood	blood
13	chr14:65996400-66004200	Weak transcription	Fetal Stomach	stomach
14	chr14:65997400-65998200	Enhancers	GM12878-XiMat	blood
15	chr14:65997400-65998400	Enhancers	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links