Variant report

Variant	rs4928005
Chromosome Location	chr3:54202453-54202454
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11719463	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719497	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530734	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4077945	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4440155	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4927999	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4928000	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4928002	0.89[EUR][1000 genomes]
rs6445629	0.96[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs6764560	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6797113	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799361	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs6803038	0.91[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6803515	1.00[CEU][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7653627	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881700	1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap]
rs9311525	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs9809321	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846298	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9859850	0.90[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9883488	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4928005	GPR183	trans	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54198000-54202800	Weak transcription	Lung	lung
2	chr3:54199000-54202600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:54200400-54205400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:54200400-54214800	Weak transcription	Psoas Muscle	Psoas
5	chr3:54201400-54202800	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr3:54202000-54203000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr3:54202000-54203000	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr3:54202200-54203000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr3:54202200-54203200	Enhancers	H9 Cell Line	embryonic stem cell
10	chr3:54202200-54203200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr3:54202200-54203200	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr3:54202400-54203000	Enhancers	H1 Cell Line	embryonic stem cell
13	chr3:54202400-54203000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr3:54202400-54203400	Enhancers	HUES48 Cell Line	embryonic stem cell

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