Variant report

Variant	rs257742
Chromosome Location	chr5:15853255-15853256
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10042283	1.00[ASW][hapmap];0.91[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs10520829	0.91[CEU][hapmap];0.85[CHD][hapmap];0.91[MEX][hapmap]
rs10520830	0.87[CEU][hapmap]
rs10520831	0.87[CEU][hapmap]
rs1087196	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11749742	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11948399	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12188594	0.87[CEU][hapmap];0.80[CHD][hapmap];0.91[MEX][hapmap]
rs12517809	0.87[CEU][hapmap]
rs12653963	0.87[CEU][hapmap]
rs12655296	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13153362	0.87[CEU][hapmap]
rs13154254	0.87[CEU][hapmap]
rs13164363	0.87[CEU][hapmap];0.80[CHD][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs146351	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1505031	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs173998	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs185406	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs187705	0.96[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2089201	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs257734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs257735	0.91[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs257736	0.92[ASW][hapmap];0.91[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs257737	0.91[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs257738	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs257739	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs257740	0.91[CEU][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs257741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs257745	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs257746	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs257747	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs257748	0.91[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs257749	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs257750	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs257752	0.91[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs257753	0.91[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs257754	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs257755	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs257756	0.88[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs257757	0.91[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs257758	0.91[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs257759	0.91[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs257760	0.91[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs257761	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs257762	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs257763	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs257764	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs257765	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs257767	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs257768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs257769	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs257770	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs257771	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs257772	0.95[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs257774	0.91[CEU][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs257777	0.96[CEU][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs257778	0.96[CEU][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs257779	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs257780	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs257781	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs257782	0.91[CEU][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35573147	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35695218	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs365234	0.91[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs366760	0.91[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs389114	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs389804	0.91[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs393806	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs398082	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399259	0.96[CEU][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs402438	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs406819	0.96[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs407717	0.96[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs415718	0.91[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs416952	0.91[CEU][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs418619	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs422958	0.96[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs423447	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs428910	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs433107	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs434475	0.95[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs435109	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4410637	0.91[CEU][hapmap];0.80[CHD][hapmap];0.91[MEX][hapmap]
rs441343	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs445085	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4643955	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs560818	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62348078	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62348081	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62348083	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6870163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6874587	0.87[CEU][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs6876718	0.87[CEU][hapmap]
rs6878591	0.87[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs6878775	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs6892388	0.91[CEU][hapmap];0.91[MEX][hapmap]
rs793424	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs793425	0.85[AMR][1000 genomes];0.89[EUR][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	nsv516929	chr5:15087791-15870300	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1023068	chr5:15095221-15863583	Enhancers Weak transcription Active TSS Strong transcription Flanking 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	13 gene(s)	inside rSNPs	diseases
3	nsv869040	chr5:15097602-15866117	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1028089	chr5:15636285-15883910	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv537676	chr5:15636285-15883910	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1024248	chr5:15638067-15863583	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv537677	chr5:15638067-15863583	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv880755	chr5:15670377-15938553	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
9	esv2763894	chr5:15714022-15863332	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1031483	chr5:15738485-15926083	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs257742	MARCH11	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15842400-15853600	Weak transcription	Fetal Stomach	stomach
2	chr5:15849800-15854600	Enhancers	Fetal Heart	heart
3	chr5:15850400-15853800	Enhancers	Adipose Nuclei	Adipose
4	chr5:15851200-15856400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr5:15851400-15854600	Enhancers	Fetal Lung	lung
6	chr5:15851400-15856400	Weak transcription	Aorta	Aorta
7	chr5:15851800-15870400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr5:15852400-15854000	Enhancers	Liver	Liver
9	chr5:15852800-15854600	Weak transcription	HUVEC	blood vessel
10	chr5:15853000-15853600	Enhancers	Right Atrium	heart
11	chr5:15853000-15854000	Enhancers	Left Ventricle	heart
12	chr5:15853200-15853400	Enhancers	Ovary	ovary
13	chr5:15853200-15853600	Enhancers	Spleen	Spleen
14	chr5:15853200-15853800	Weak transcription	Colon Smooth Muscle	Colon
15	chr5:15853200-15853800	Enhancers	Lung	lung
16	chr5:15853200-15853800	Enhancers	Psoas Muscle	Psoas
17	chr5:15853200-15853800	Enhancers	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links