Variant report

Variant	rs540141
Chromosome Location	chr11:63050218-63050219
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 188 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:177)

rs_ID	r²[population]
rs10750995	0.84[ASN][1000 genomes]
rs10792403	0.84[ASN][1000 genomes]
rs10792404	0.84[ASN][1000 genomes]
rs10792406	0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10897380	0.84[ASN][1000 genomes]
rs10897381	0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10897382	0.84[ASN][1000 genomes]
rs10897383	0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10897384	0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10897390	0.85[ASN][1000 genomes]
rs10897392	0.85[ASN][1000 genomes]
rs10897396	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10897397	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10897399	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10897407	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs11231391	0.84[ASN][1000 genomes]
rs11231392	0.84[ASN][1000 genomes]
rs11231394	0.84[ASN][1000 genomes]
rs11231395	0.83[ASN][1000 genomes]
rs11231396	0.84[ASN][1000 genomes]
rs11231397	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11231403	0.84[ASN][1000 genomes]
rs11231409	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11231410	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11231411	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11231412	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11231413	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11231414	0.87[ASN][1000 genomes]
rs11231417	0.86[ASN][1000 genomes]
rs11231418	0.86[ASN][1000 genomes]
rs11231419	0.86[ASN][1000 genomes]
rs11494212	0.81[ASN][1000 genomes]
rs1152244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1152245	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1152246	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11524468	0.85[ASN][1000 genomes]
rs11524903	0.87[ASN][1000 genomes]
rs11537206	0.83[ASN][1000 genomes]
rs1193642	0.87[ASN][1000 genomes]
rs1193645	0.87[ASN][1000 genomes]
rs1193646	0.87[ASN][1000 genomes]
rs1193718	0.99[ASN][1000 genomes]
rs1193726	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1193729	0.99[ASN][1000 genomes]
rs1193733	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1193772	0.90[ASN][1000 genomes]
rs1193774	0.90[ASN][1000 genomes]
rs1193775	0.90[ASN][1000 genomes]
rs1193786	0.82[ASN][1000 genomes]
rs1193787	0.85[ASN][1000 genomes]
rs1193789	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1193856	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1193891	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1193892	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1193893	0.87[ASN][1000 genomes]
rs1193894	0.87[ASN][1000 genomes]
rs1193896	0.86[ASN][1000 genomes]
rs1193897	0.84[ASN][1000 genomes]
rs1193904	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1193905	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1201559	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1205166	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1205186	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1211246	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1211550	0.85[ASN][1000 genomes]
rs12224010	0.84[ASN][1000 genomes]
rs12225186	0.84[ASN][1000 genomes]
rs12283500	0.81[ASN][1000 genomes]
rs12416737	0.87[ASN][1000 genomes]
rs12417255	0.87[ASN][1000 genomes]
rs12417508	0.85[ASN][1000 genomes]
rs12418081	0.87[ASN][1000 genomes]
rs12574223	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12574967	0.87[ASN][1000 genomes]
rs12576556	0.86[ASN][1000 genomes]
rs12577849	0.86[ASN][1000 genomes]
rs1300795	0.87[ASN][1000 genomes]
rs1300796	0.85[ASN][1000 genomes]
rs1300798	0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1308010	0.85[ASN][1000 genomes]
rs1404608	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1525064	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1525071	0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1608760	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1723213	0.99[ASN][1000 genomes]
rs1723219	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1783634	0.99[ASN][1000 genomes]
rs1783652	0.86[ASN][1000 genomes]
rs1783654	0.87[ASN][1000 genomes]
rs1789327	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1789334	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1790218	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790226	0.86[ASN][1000 genomes]
rs1830026	0.85[ASN][1000 genomes]
rs1852067	0.85[ASN][1000 genomes]
rs1939739	0.84[ASN][1000 genomes]
rs1944086	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1944091	0.87[ASN][1000 genomes]
rs1997038	0.85[ASN][1000 genomes]
rs2155316	0.84[ASN][1000 genomes]
rs2186719	0.84[ASN][1000 genomes]
rs2186721	0.84[ASN][1000 genomes]
rs2222591	0.84[ASN][1000 genomes]
rs2226866	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2317089	0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2317090	0.84[ASN][1000 genomes]
rs2317093	0.84[ASN][1000 genomes]
rs2510590	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3891629	0.90[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs3915142	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3937020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4000269	0.85[ASN][1000 genomes]
rs4258381	0.85[ASN][1000 genomes]
rs4315076	0.87[ASN][1000 genomes]
rs4337047	0.84[ASN][1000 genomes]
rs4344494	0.85[ASN][1000 genomes]
rs4445638	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4570581	0.85[ASN][1000 genomes]
rs474096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs474191	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs474815	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs474874	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs483012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs486460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488803	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs494608	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs4963252	0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4963385	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.90[ASN][1000 genomes]
rs499003	0.82[EUR][1000 genomes]
rs505653	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs513338	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs515213	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs516536	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs517655	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs523928	0.88[ASN][1000 genomes]
rs524724	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs527027	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527869	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs532085	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs534799	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs537194	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs543429	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs548885	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs549144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs554430	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs556730	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs557658	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs557879	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs558472	0.81[EUR][1000 genomes]
rs55963399	0.84[ASN][1000 genomes]
rs564917	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs565787	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs566456	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs572017	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs575009	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs576641	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58347848	0.82[ASN][1000 genomes]
rs58673340	0.87[ASN][1000 genomes]
rs59019924	0.85[ASN][1000 genomes]
rs59626188	0.87[ASN][1000 genomes]
rs60090619	0.87[ASN][1000 genomes]
rs60477987	0.87[ASN][1000 genomes]
rs61928158	0.87[ASN][1000 genomes]
rs6591771	0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs6591778	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs688999	0.82[EUR][1000 genomes]
rs7115707	0.84[ASN][1000 genomes]
rs7126435	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7130728	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs722508	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs7925045	0.83[ASN][1000 genomes]
rs7925760	0.83[ASN][1000 genomes]
rs7932800	0.86[ASN][1000 genomes]
rs7938140	0.90[ASN][1000 genomes]
rs7938146	0.87[ASN][1000 genomes]
rs7938863	0.84[ASN][1000 genomes]
rs7949840	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv897627	chr11:62984868-63119486	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
10	esv2757449	chr11:63044992-63126854	ZNF genes & repeats Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv2759833	chr11:63044992-63126854	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs540141	SLC22A10	cis	Esophagus Muscularis	GTEx
rs540141	SLC22A25	cis	Esophagus Mucosa	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63046600-63050400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:63050200-63050400	Bivalent Enhancer	Esophagus	oesophagus
3	chr11:63050200-63050400	Enhancers	HepG2	liver
4	chr11:63050200-63050800	Enhancers	Pancreas	Pancrea
5	chr11:63050200-63050800	Active TSS	Spleen	Spleen
6	chr11:63050200-63051000	Enhancers	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links