Variant report

Variant	rs7664129
Chromosome Location	chr4:158969682-158969683
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10021199	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10024235	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10517685	0.86[ASN][1000 genomes]
rs10517686	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[ASN][1000 genomes]
rs11100152	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs11939690	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs13130880	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13137328	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13137541	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036992	0.86[ASN][1000 genomes]
rs17036995	0.86[ASN][1000 genomes]
rs17037201	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs17037232	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs17212066	0.86[ASN][1000 genomes]
rs17212714	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs17271385	0.86[ASN][1000 genomes]
rs17279270	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs2594745	0.84[AMR][1000 genomes]
rs2594759	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2594760	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2594761	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2594762	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2594764	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2594765	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2594768	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2594770	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2725490	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2725491	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2725492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2725493	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2725494	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2725495	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2725496	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2725497	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2725498	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2725500	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2725504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2725505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2725506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2725507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2725508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2725519	0.84[AMR][1000 genomes]
rs28373894	0.82[AMR][1000 genomes]
rs28448481	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2881374	0.86[ASN][1000 genomes]
rs4234916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4259109	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4349642	0.90[AMR][1000 genomes]
rs4355442	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4401497	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4404597	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4425428	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4443327	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4447905	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4455468	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4460049	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4484350	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4495089	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4505875	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4508943	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4510503	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4519842	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4549446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4549447	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4571380	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4571382	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4580697	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4608853	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611971	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4615227	0.90[AMR][1000 genomes]
rs4618359	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55800218	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58537354	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6536289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6536290	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6536291	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6536294	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815974	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820988	0.91[CEU][hapmap]
rs6829412	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6830333	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6834839	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs6837943	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs72689905	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72689908	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72689912	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72691603	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691606	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691610	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72691615	0.86[ASN][1000 genomes]
rs72691620	0.86[ASN][1000 genomes]
rs72691622	0.86[ASN][1000 genomes]
rs72691626	0.86[ASN][1000 genomes]
rs72691627	0.86[ASN][1000 genomes]
rs72691629	0.86[ASN][1000 genomes]
rs72691631	0.86[ASN][1000 genomes]
rs72691632	0.86[ASN][1000 genomes]
rs72691633	0.86[ASN][1000 genomes]
rs72691634	0.86[ASN][1000 genomes]
rs72691636	0.86[ASN][1000 genomes]
rs72691649	0.81[AMR][1000 genomes]
rs72695012	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72695013	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72695014	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72695016	0.90[AMR][1000 genomes]
rs72695017	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72695018	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72695019	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72695020	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72695025	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72695027	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7661831	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7678302	0.83[CEU][hapmap]
rs7685237	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7689949	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7698469	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9997618	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7664129	DKFZp434L142	cis	multi-tissue	Pritchard
rs7664129	RP11-597D13.9	cis	Skin Sun Exposed Lower leg	GTEx
rs7664129	FLJ11155	cis	multi-tissue	Pritchard
rs7664129	RP11-597D13.9	cis	Esophagus Muscularis	GTEx
rs7664129	TMEM144	cis	Esophagus Muscularis	GTEx
rs7664129	FAM198B	cis	brain	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:158964800-158971800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr4:158965000-158971800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:158965000-158971800	Weak transcription	NHDF-Ad	bronchial
4	chr4:158968000-158971600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:158968000-158972000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr4:158968000-158972000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr4:158968000-158972000	Weak transcription	HSMM	muscle
8	chr4:158968000-158972000	Weak transcription	HSMMtube	muscle
9	chr4:158968000-158972000	Weak transcription	Osteobl	bone

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