Variant report

Variant	rs625897
Chromosome Location	chr6:141119905-141119906
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 138 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10499221	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs1074714	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11155126	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11155127	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1206455	0.91[ASN][1000 genomes]
rs1402509	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1521136	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1521137	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1568482	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs1568483	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1607921	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2143604	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2206790	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223705	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs582203	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs583551	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs584505	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs584727	0.91[ASN][1000 genomes]
rs585656	0.85[ASN][1000 genomes]
rs586523	0.90[ASN][1000 genomes]
rs587825	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs590595	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs593101	0.93[ASN][1000 genomes]
rs594332	0.93[ASN][1000 genomes]
rs594433	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594761	0.93[ASN][1000 genomes]
rs596276	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596721	0.92[ASN][1000 genomes]
rs599266	0.86[ASN][1000 genomes]
rs599901	0.92[ASN][1000 genomes]
rs599928	0.92[ASN][1000 genomes]
rs601084	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs605384	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs606180	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs607855	0.93[ASN][1000 genomes]
rs608138	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs609656	0.91[ASN][1000 genomes]
rs610619	0.88[ASN][1000 genomes]
rs611438	0.93[ASN][1000 genomes]
rs612305	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs612960	0.90[ASN][1000 genomes]
rs613070	0.94[ASN][1000 genomes]
rs613253	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613931	0.94[ASN][1000 genomes]
rs615207	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs617946	0.93[ASN][1000 genomes]
rs618406	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs618795	0.93[ASN][1000 genomes]
rs620151	0.93[ASN][1000 genomes]
rs623190	0.93[ASN][1000 genomes]
rs623571	0.93[ASN][1000 genomes]
rs626931	0.90[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs627452	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs627812	0.93[ASN][1000 genomes]
rs629205	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs629223	0.94[ASN][1000 genomes]
rs629607	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs630383	0.93[ASN][1000 genomes]
rs630596	0.93[ASN][1000 genomes]
rs631576	0.93[ASN][1000 genomes]
rs632617	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs633796	0.93[ASN][1000 genomes]
rs637822	0.93[ASN][1000 genomes]
rs640567	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641364	0.92[ASN][1000 genomes]
rs641720	0.91[ASN][1000 genomes]
rs643403	0.94[ASN][1000 genomes]
rs643558	0.91[ASN][1000 genomes]
rs644443	0.93[ASN][1000 genomes]
rs644638	0.91[ASN][1000 genomes]
rs646921	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs647781	0.93[ASN][1000 genomes]
rs647875	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs650907	0.93[ASN][1000 genomes]
rs653656	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655154	0.93[ASN][1000 genomes]
rs655386	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656160	0.90[ASN][1000 genomes]
rs656512	0.89[ASN][1000 genomes]
rs6570415	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6570416	0.81[EUR][1000 genomes]
rs6570417	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6570418	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6570419	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6570420	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659647	0.94[ASN][1000 genomes]
rs664281	0.93[ASN][1000 genomes]
rs665541	0.93[ASN][1000 genomes]
rs669528	0.90[ASN][1000 genomes]
rs670375	0.94[ASN][1000 genomes]
rs672301	0.92[ASN][1000 genomes]
rs672906	0.93[ASN][1000 genomes]
rs673799	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs677319	0.90[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs681758	0.93[ASN][1000 genomes]
rs686347	0.84[AFR][1000 genomes]
rs687815	0.93[ASN][1000 genomes]
rs687879	0.93[ASN][1000 genomes]
rs688310	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6911804	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6936610	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7738869	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7743346	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7759288	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7763057	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774722	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9484432	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9495815	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9495827	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs985070	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs985071	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs985072	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817390	chr6:140558103-141166039	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1031320	chr6:140798377-141156979	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1026042	chr6:140813667-141414842	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv869287	chr6:140826709-141407102	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv886697	chr6:140878731-141182209	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv886698	chr6:140878731-141194073	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv886699	chr6:140878731-141209198	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
8	nsv886705	chr6:140902819-141194073	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
9	nsv886706	chr6:140902819-141209198	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
10	nsv886707	chr6:140902819-141301076	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
11	nsv886710	chr6:140911389-141194073	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
12	nsv886711	chr6:140911389-141209198	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
13	nsv604775	chr6:140948427-141219060	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
14	nsv886715	chr6:140968292-141188478	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
15	nsv886716	chr6:140968292-141209198	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
16	nsv886718	chr6:141003924-141149548	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
17	nsv1021789	chr6:141024733-141284394	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv1019459	chr6:141051249-141862727	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
19	nsv538453	chr6:141051249-141862727	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
20	nsv532070	chr6:141057326-141865359	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
21	nsv604779	chr6:141063235-141241876	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	esv2830172	chr6:141079124-141364472	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv1025922	chr6:141090901-141865360	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
24	nsv538454	chr6:141090901-141865360	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
25	esv3392456	chr6:141112308-141137774	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases
26	nsv966687	chr6:141114750-141127713	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs625897	IL20RA	cis	parietal	SCAN
rs625897	LTV1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:141089600-141121800	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links