Variant report

Variant	rs2389882
Chromosome Location	chr4:120566733-120566734
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10006525	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs10006706	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs10009566	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10009626	0.82[CEU][hapmap];0.95[JPT][hapmap]
rs10012252	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10013305	0.83[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs10017335	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs10018280	0.81[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs10019674	0.83[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs10022185	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10030660	0.82[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs10031483	0.83[CEU][hapmap];0.95[JPT][hapmap]
rs10034450	0.87[CEU][hapmap]
rs10050092	0.83[CHB][hapmap]
rs1010739	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs1010740	0.83[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs10518328	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs10518329	0.90[JPT][hapmap];0.81[TSI][hapmap]
rs11098530	0.83[CEU][hapmap]
rs11098531	0.88[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11098534	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1155576	0.83[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs11723090	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11729521	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs11731756	0.83[CEU][hapmap];0.95[JPT][hapmap]
rs11734241	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs11737395	0.88[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11933966	0.83[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap]
rs11935596	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11947234	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs12498599	0.83[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs12499377	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12502423	0.83[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs12504773	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12505735	0.85[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs12507964	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs12508504	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs12510138	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs12512646	0.83[CEU][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs12642411	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13122709	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13128602	0.83[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs13134665	0.83[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs13136462	0.84[EUR][1000 genomes]
rs13149407	0.90[JPT][hapmap]
rs1383532	0.83[CEU][hapmap];0.80[CHB][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs1480931	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs1480936	0.82[CHD][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap]
rs1480940	0.83[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs1552092	0.84[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs1552095	0.83[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs17006190	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs17050695	0.81[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs17051352	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17051356	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2127821	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs2127823	0.83[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs2170276	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2291185	0.83[CEU][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs2306456	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2389803	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs2389809	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2389880	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2389885	0.84[EUR][1000 genomes]
rs2389886	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2389887	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28394116	0.82[EUR][1000 genomes]
rs28535956	0.83[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs28578366	0.83[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs28787668	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28850368	0.88[ASN][1000 genomes]
rs2892848	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap]
rs34278750	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34835603	0.88[ASN][1000 genomes]
rs3733519	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs3733520	0.83[CEU][hapmap]
rs3733524	0.83[CEU][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs3736115	0.83[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs3756156	0.94[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs3775841	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs3775843	0.83[CEU][hapmap];0.95[JPT][hapmap]
rs3775844	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs3775845	0.82[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs3775848	0.83[CEU][hapmap];0.95[JPT][hapmap]
rs3775852	0.82[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs3806808	0.85[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs3822192	0.83[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs3822194	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs3822195	0.81[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs4504231	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4833624	0.83[CEU][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs6534139	0.83[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs6832740	0.81[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs6834796	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs6835635	0.83[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs6848389	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs6849171	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs6849561	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs6853998	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs7659501	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs7664440	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7665125	0.90[JPT][hapmap]
rs7671096	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7676296	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7680914	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7681544	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs7687843	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs7688802	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs7692994	0.89[JPT][hapmap]
rs7695292	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7695620	0.83[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap]
rs7699064	0.83[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap]
rs9884402	0.83[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap]
rs9997631	0.86[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs9998585	0.83[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1802546	chr4:120558608-120675026	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2389882	RP11-33B1.1	cis	Heart Left Ventricle	GTEx
rs2389882	LOC644243	trans	multi-tissue	Pritchard
rs2389882	RP11-33B1.4	cis	Whole Blood	GTEx
rs2389882	RP11-33B1.1	cis	Whole Blood	GTEx
rs2389882	RP11-33B1.1	cis	lung	GTEx
rs2389882	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_chr	lymphoblastoid	RTeQTL
rs2389882	C4orf3	cis	cerebellum	SCAN
rs2389882	QRFPR	cis	parietal	SCAN
rs2389882	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs2389882	RP11-33B1.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120559800-120567800	Weak transcription	Osteobl	bone
2	chr4:120560000-120567800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:120565200-120567600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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