Variant report

Variant	rs12417508
Chromosome Location	chr11:62976503-62976504
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 183 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:173)

rs_ID	r²[population]
rs10750995	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10792403	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10792404	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10792406	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10897380	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10897381	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10897382	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10897383	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10897384	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10897387	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10897390	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10897392	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10897396	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10897397	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10897399	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1122524	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11231391	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231392	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231394	0.99[ASN][1000 genomes]
rs11231395	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11231396	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231397	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231403	0.99[ASN][1000 genomes]
rs11231406	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11231409	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231410	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231411	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231412	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231413	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231414	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231415	0.85[AFR][1000 genomes]
rs11231417	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11231418	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11231419	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11494212	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1152244	0.85[ASN][1000 genomes]
rs1152245	0.86[ASN][1000 genomes]
rs1152246	0.86[ASN][1000 genomes]
rs11524468	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11524903	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11537206	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11559570	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1193642	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1193645	0.99[ASN][1000 genomes]
rs1193646	0.99[ASN][1000 genomes]
rs1193718	0.87[ASN][1000 genomes]
rs1193726	0.86[ASN][1000 genomes]
rs1193729	0.85[ASN][1000 genomes]
rs1193733	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1193772	0.96[ASN][1000 genomes]
rs1193774	0.96[ASN][1000 genomes]
rs1193775	0.96[ASN][1000 genomes]
rs1193789	0.86[ASN][1000 genomes]
rs1193856	0.95[ASN][1000 genomes]
rs1193891	0.96[ASN][1000 genomes]
rs1193892	0.99[ASN][1000 genomes]
rs1193893	0.99[ASN][1000 genomes]
rs1193894	0.99[ASN][1000 genomes]
rs1193896	0.98[ASN][1000 genomes]
rs1193897	0.96[ASN][1000 genomes]
rs1193904	0.85[ASN][1000 genomes]
rs1193905	0.85[ASN][1000 genomes]
rs1201559	0.87[ASN][1000 genomes]
rs1205166	0.86[ASN][1000 genomes]
rs1205186	0.86[ASN][1000 genomes]
rs1211246	0.96[ASN][1000 genomes]
rs1211550	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12224010	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12225186	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12416737	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12417255	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12418081	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12574223	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12574967	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12576556	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12577849	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12785663	0.82[ASN][1000 genomes]
rs1300795	0.99[ASN][1000 genomes]
rs1300796	1.00[ASN][1000 genomes]
rs1300798	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1308010	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1404608	0.87[ASN][1000 genomes]
rs1525064	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1525071	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1608760	0.85[ASN][1000 genomes]
rs1723213	0.87[ASN][1000 genomes]
rs1723219	0.99[ASN][1000 genomes]
rs1783634	0.87[ASN][1000 genomes]
rs1783652	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1783654	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1789327	0.85[ASN][1000 genomes]
rs1789334	0.87[ASN][1000 genomes]
rs1790218	0.85[ASN][1000 genomes]
rs1830026	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1852067	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1939739	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1944091	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1944092	0.82[ASN][1000 genomes]
rs1997038	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2155316	0.99[ASN][1000 genomes]
rs2186719	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2186721	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2222591	0.99[ASN][1000 genomes]
rs2226866	0.86[ASN][1000 genomes]
rs2317089	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2317090	0.99[ASN][1000 genomes]
rs2317093	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2510590	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2510591	0.83[ASN][1000 genomes]
rs3891629	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3915142	0.87[ASN][1000 genomes]
rs3937020	0.85[ASN][1000 genomes]
rs4000269	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4060975	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4258381	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4315076	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4337047	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4344494	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4445638	0.86[ASN][1000 genomes]
rs474096	0.87[ASN][1000 genomes]
rs474191	0.87[ASN][1000 genomes]
rs474815	0.83[ASN][1000 genomes]
rs474874	0.87[ASN][1000 genomes]
rs483012	0.87[ASN][1000 genomes]
rs486460	0.85[ASN][1000 genomes]
rs4963252	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4963380	0.92[ASN][1000 genomes]
rs4963381	0.92[ASN][1000 genomes]
rs4963385	0.96[ASN][1000 genomes]
rs505653	0.87[ASN][1000 genomes]
rs513338	0.87[ASN][1000 genomes]
rs515213	0.87[ASN][1000 genomes]
rs524724	0.87[ASN][1000 genomes]
rs527027	0.85[ASN][1000 genomes]
rs527869	0.85[ASN][1000 genomes]
rs532085	0.87[ASN][1000 genomes]
rs534799	0.87[ASN][1000 genomes]
rs540141	0.85[ASN][1000 genomes]
rs543429	0.85[ASN][1000 genomes]
rs548885	0.87[ASN][1000 genomes]
rs549144	0.84[ASN][1000 genomes]
rs554430	0.85[ASN][1000 genomes]
rs557658	0.87[ASN][1000 genomes]
rs557879	0.87[ASN][1000 genomes]
rs55963399	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56030503	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs565787	0.87[ASN][1000 genomes]
rs572017	0.87[ASN][1000 genomes]
rs575009	0.87[ASN][1000 genomes]
rs576641	0.87[ASN][1000 genomes]
rs58347848	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58673340	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59019924	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59626188	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60090619	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60477987	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61928110	0.87[ASN][1000 genomes]
rs61928158	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6591771	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6591772	0.90[ASN][1000 genomes]
rs6591778	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7115707	0.99[ASN][1000 genomes]
rs7126435	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7130728	0.87[ASN][1000 genomes]
rs7925045	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7925760	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7928993	0.92[ASN][1000 genomes]
rs7929092	0.87[ASN][1000 genomes]
rs7932800	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7938140	0.96[ASN][1000 genomes]
rs7938146	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7938863	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7949840	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34011	chr11:62652779-62993702	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1045308	chr11:62803635-63109338	Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv541059	chr11:62803635-63109338	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv555177	chr11:62847518-63110569	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1049725	chr11:62848172-63057827	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv541060	chr11:62848172-63057827	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1047571	chr11:62848172-63109338	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv430397	chr11:62852616-63072310	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv2753282	chr11:62883681-62986146	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	esv3363793	chr11:62975063-62981962	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12417508	SLC22A25	cis	Esophagus Mucosa	GTEx
rs12417508	SLC22A10	cis	Esophagus Muscularis	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62973600-62978800	Strong transcription	Liver	Liver
2	chr11:62975400-62977400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr11:62975400-62978600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr11:62975600-62976800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr11:62975600-62977000	Enhancers	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links