Variant report

Variant	rs6445629
Chromosome Location	chr3:54188227-54188228
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11130398	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs11713312	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11719463	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs11719497	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs11914927	0.82[ASN][1000 genomes]
rs11917010	0.84[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11926147	0.86[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12635465	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1530734	0.96[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17802213	0.90[JPT][hapmap]
rs2067581	0.84[JPT][hapmap]
rs28613537	0.82[ASN][1000 genomes]
rs4077945	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs4440155	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4927999	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4928000	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4928002	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4928005	0.96[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs56349750	0.82[ASN][1000 genomes]
rs59072955	0.82[ASN][1000 genomes]
rs6764560	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6794229	0.84[JPT][hapmap]
rs6797113	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs6799361	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6803515	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73085924	0.82[ASN][1000 genomes]
rs73085925	0.80[ASN][1000 genomes]
rs7653627	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs881700	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs9311525	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs9809321	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs9846298	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9883488	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1014157	chr3:54168755-54332321	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6445629	GPR183	trans	lymphoblastoid	seeQTL
rs6445629	IQCF1	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54181000-54195000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:54181600-54192000	Weak transcription	Stomach Smooth Muscle	stomach

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