Variant report

Variant	rs158988
Chromosome Location	chr5:57972721-57972722
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1158196	0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs12054892	0.81[JPT][hapmap]
rs12653046	0.86[JPT][hapmap]
rs149351	0.90[AFR][1000 genomes]
rs158986	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs158991	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158992	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs158994	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs158995	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158998	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs158999	0.96[LWK][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes]
rs159001	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs159009	0.92[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16877131	0.95[YRI][hapmap]
rs176637	0.80[AFR][1000 genomes]
rs1833613	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2591913	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs2591921	0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2591923	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2662624	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs290572	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs290573	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs292994	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs292995	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs293004	0.91[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs293005	0.89[LWK][hapmap]
rs293016	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs293017	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs293019	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs293021	0.92[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs293024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293028	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs293030	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs293031	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs49960	0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs58662773	0.92[AFR][1000 genomes]
rs6898044	0.81[JPT][hapmap]
rs7723730	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1029145	chr5:57905821-58141221	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830311	chr5:57912546-58105636	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv4845	chr5:57949493-57994156	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs158988	MAP3K1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57967400-57973600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:57967400-57977800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr5:57971800-57978400	Enhancers	HUVEC	blood vessel
4	chr5:57972000-57972800	Weak transcription	Spleen	Spleen

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