Variant report

Variant	rs28373894
Chromosome Location	chr4:158897697-158897698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10024235	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13130880	0.82[AMR][1000 genomes]
rs13137328	0.82[AMR][1000 genomes]
rs13137541	0.82[AMR][1000 genomes]
rs2594745	0.85[AMR][1000 genomes]
rs2594759	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2594760	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2594761	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2594762	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2594764	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2594765	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2594768	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2594770	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2725490	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2725491	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2725492	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2725493	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2725494	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2725495	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2725496	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2725497	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2725498	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2725500	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2725504	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2725505	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2725506	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2725507	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2725508	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2725519	0.85[AMR][1000 genomes]
rs28448481	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4234916	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4259109	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4349642	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4355442	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4401497	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4404597	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4425428	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4443327	0.82[AMR][1000 genomes]
rs4447905	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4455468	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4460049	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4484350	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4495089	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4505875	0.88[AMR][1000 genomes]
rs4508943	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4510503	0.82[AMR][1000 genomes]
rs4519842	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4549446	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4549447	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4571380	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4571382	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4580697	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4608853	0.82[AMR][1000 genomes]
rs4611971	0.88[AMR][1000 genomes]
rs4615227	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4618359	0.88[AMR][1000 genomes]
rs55800218	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58537354	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6536289	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6536290	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6536291	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6536294	0.82[AMR][1000 genomes]
rs6815974	0.82[AMR][1000 genomes]
rs6829412	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6830333	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72689905	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72689908	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72689912	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72691603	0.82[AMR][1000 genomes]
rs72695012	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72695013	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72695014	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72695016	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72695017	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72695018	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72695019	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72695020	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72695025	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72695027	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7661831	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7664129	0.82[AMR][1000 genomes]
rs7685237	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7689949	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7698469	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9997618	0.82[AMR][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	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1025064	chr4:158719316-158898333	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv881288	chr4:158891733-159028080	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28373894	RP11-597D13.9	cis	Esophagus Muscularis	GTEx
rs28373894	RP11-597D13.9	cis	Skin Sun Exposed Lower leg	GTEx
rs28373894	TMEM144	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:158893400-158901200	Weak transcription	Aorta	Aorta
2	chr4:158895800-158900000	Weak transcription	Fetal Intestine Small	intestine
3	chr4:158897200-158899800	Weak transcription	Psoas Muscle	Psoas
4	chr4:158897600-158898800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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