Variant report

Variant	rs7646139
Chromosome Location	chr3:136783679-136783680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1017491	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1023765	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935221	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13098923	0.82[AMR][1000 genomes]
rs1351892	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1470143	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1484787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1484794	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3899122	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4678286	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6439683	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6439685	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6439686	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6773448	0.85[AMR][1000 genomes]
rs6781928	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6806914	0.83[AMR][1000 genomes]
rs6807138	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6808049	0.85[AMR][1000 genomes]
rs6808051	0.85[AMR][1000 genomes]
rs7627723	0.83[AMR][1000 genomes]
rs9289525	0.83[AMR][1000 genomes]
rs969329	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9818918	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9819250	0.86[AMR][1000 genomes]
rs9822931	0.82[AMR][1000 genomes]
rs9826507	0.85[AMR][1000 genomes]
rs9838513	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9843104	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9843219	0.82[AMR][1000 genomes]
rs9874836	0.85[AMR][1000 genomes]
rs9882135	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524856	chr3:136693459-137190765	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1012111	chr3:136695367-137343430	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7646139	GRK7	cis	cerebellum	SCAN
rs7646139	BPESC1	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136757000-136794000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:136765000-136784200	Weak transcription	Esophagus	oesophagus
3	chr3:136769400-136796200	Weak transcription	NHEK	skin
4	chr3:136782000-136804600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:136782600-136785800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:136783400-136784000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr3:136783400-136784000	Enhancers	GM12878-XiMat	blood
8	chr3:136783400-136785800	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr3:136783400-136786200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:136783600-136783800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
11	chr3:136783600-136784600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr3:136783600-136785800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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