Variant report

Variant	rs12504773
Chromosome Location	chr4:120562149-120562150
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 135 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10008791	0.81[EUR][1000 genomes]
rs10009566	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10009626	0.81[EUR][1000 genomes]
rs10012252	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10013305	0.81[EUR][1000 genomes]
rs10018280	0.81[EUR][1000 genomes]
rs10019674	0.81[EUR][1000 genomes]
rs10022185	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10030660	0.81[EUR][1000 genomes]
rs10034450	0.81[EUR][1000 genomes]
rs10050092	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1010739	0.81[EUR][1000 genomes]
rs1010740	0.81[EUR][1000 genomes]
rs11098531	0.81[EUR][1000 genomes]
rs11098532	0.83[EUR][1000 genomes]
rs11098534	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1155576	0.81[EUR][1000 genomes]
rs11723090	0.83[EUR][1000 genomes]
rs11731756	0.81[EUR][1000 genomes]
rs11736416	0.81[EUR][1000 genomes]
rs11737395	0.88[EUR][1000 genomes]
rs11933966	0.81[EUR][1000 genomes]
rs11947234	0.81[EUR][1000 genomes]
rs12498539	0.81[EUR][1000 genomes]
rs12498599	0.81[EUR][1000 genomes]
rs12499377	0.86[EUR][1000 genomes]
rs12502389	0.81[EUR][1000 genomes]
rs12505735	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12512646	0.84[EUR][1000 genomes]
rs12642411	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13101722	0.85[ASN][1000 genomes]
rs13122709	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13128602	0.81[EUR][1000 genomes]
rs13134665	0.81[EUR][1000 genomes]
rs13136462	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13140391	0.87[EUR][1000 genomes]
rs13140409	0.87[EUR][1000 genomes]
rs13149407	0.81[EUR][1000 genomes]
rs1383532	0.81[EUR][1000 genomes]
rs1383533	0.81[EUR][1000 genomes]
rs1480936	0.81[EUR][1000 genomes]
rs1480939	0.81[EUR][1000 genomes]
rs1480940	0.81[EUR][1000 genomes]
rs1552092	0.83[EUR][1000 genomes]
rs1552095	0.81[EUR][1000 genomes]
rs17050695	0.83[EUR][1000 genomes]
rs17051352	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17051356	0.85[EUR][1000 genomes]
rs2086450	0.81[EUR][1000 genomes]
rs2127823	0.83[EUR][1000 genomes]
rs2170276	0.83[EUR][1000 genomes]
rs2291185	0.81[EUR][1000 genomes]
rs2306456	0.81[EUR][1000 genomes]
rs2306457	0.81[EUR][1000 genomes]
rs2389874	0.85[ASN][1000 genomes]
rs2389879	0.85[ASN][1000 genomes]
rs2389880	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2389882	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2389885	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2389886	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2389887	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28394116	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28535956	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28578366	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28718422	0.80[EUR][1000 genomes]
rs28735358	0.81[EUR][1000 genomes]
rs28787668	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28850368	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34278750	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34308924	0.83[EUR][1000 genomes]
rs34835603	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34868248	0.81[EUR][1000 genomes]
rs36040693	0.81[EUR][1000 genomes]
rs3733525	0.81[EUR][1000 genomes]
rs3736115	0.83[EUR][1000 genomes]
rs3756156	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3775841	0.81[EUR][1000 genomes]
rs3775843	0.81[EUR][1000 genomes]
rs3775844	0.81[EUR][1000 genomes]
rs3775845	0.81[EUR][1000 genomes]
rs3775847	0.81[EUR][1000 genomes]
rs3775848	0.81[EUR][1000 genomes]
rs3775849	0.81[EUR][1000 genomes]
rs3775852	0.81[EUR][1000 genomes]
rs3775854	0.81[EUR][1000 genomes]
rs3775858	0.83[EUR][1000 genomes]
rs3806808	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3822190	0.81[EUR][1000 genomes]
rs3822191	0.81[EUR][1000 genomes]
rs3822192	0.81[EUR][1000 genomes]
rs3822194	0.81[EUR][1000 genomes]
rs3822195	0.81[EUR][1000 genomes]
rs4504231	0.86[EUR][1000 genomes]
rs4596225	0.84[EUR][1000 genomes]
rs4833624	0.84[EUR][1000 genomes]
rs4998488	0.85[EUR][1000 genomes]
rs55825515	0.81[EUR][1000 genomes]
rs58452170	0.81[EUR][1000 genomes]
rs58583086	0.85[ASN][1000 genomes]
rs59732491	0.83[EUR][1000 genomes]
rs59867181	0.85[ASN][1000 genomes]
rs6534139	0.81[EUR][1000 genomes]
rs6534140	0.81[EUR][1000 genomes]
rs6534141	0.82[EUR][1000 genomes]
rs6534149	0.85[ASN][1000 genomes]
rs6829903	0.88[EUR][1000 genomes]
rs6832740	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6833334	0.87[EUR][1000 genomes]
rs6835635	0.81[EUR][1000 genomes]
rs6853998	0.81[EUR][1000 genomes]
rs6855918	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6858592	0.81[EUR][1000 genomes]
rs6858777	0.81[EUR][1000 genomes]
rs7664440	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7664986	0.81[EUR][1000 genomes]
rs7669520	0.88[EUR][1000 genomes]
rs7671096	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7676296	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7678400	0.81[EUR][1000 genomes]
rs7680914	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688802	0.81[EUR][1000 genomes]
rs7693919	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7695292	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695620	0.81[EUR][1000 genomes]
rs7699064	0.81[EUR][1000 genomes]
rs9884402	0.83[EUR][1000 genomes]
rs9995026	0.83[EUR][1000 genomes]
rs9997631	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	esv3343433	chr4:120559454-120562352	Enhancers Weak transcription	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12504773	RP11-33B1.1	cis	Whole Blood	GTEx
rs12504773	RP11-33B1.4	cis	Whole Blood	GTEx
rs12504773	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_chr	lymphoblastoid	RTeQTL
rs12504773	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs12504773	RP11-33B1.1	cis	Esophagus Mucosa	GTEx
rs12504773	RP11-33B1.1	cis	Heart Left Ventricle	GTEx
rs12504773	RP11-33B1.1	cis	lung	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	chr4:120560000-120564400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:120560000-120567800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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