Variant report

Variant	rs12747498
Chromosome Location	chr1:170440359-170440360
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:170438931..170441760-chr1:170443458..170446041,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10919407	0.86[ASN][1000 genomes]
rs10919422	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11583564	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11588124	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11589240	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11589376	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11590710	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11806866	0.90[ASN][1000 genomes]
rs12729774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12735952	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12737862	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12751882	0.86[ASN][1000 genomes]
rs12755330	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1333141	0.83[CHD][hapmap];0.89[JPT][hapmap]
rs1537389	0.83[CHD][hapmap]
rs1537394	0.89[JPT][hapmap]
rs16863369	0.90[ASN][1000 genomes]
rs1855220	0.90[ASN][1000 genomes]
rs34593046	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34597697	0.86[ASN][1000 genomes]
rs34621734	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35299255	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35329498	0.90[ASN][1000 genomes]
rs35564609	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35581791	0.88[ASN][1000 genomes]
rs4488075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61824337	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61824349	0.90[ASN][1000 genomes]
rs61824356	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61824357	0.90[ASN][1000 genomes]
rs6427248	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6427249	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6668898	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6676293	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap]
rs67243697	0.90[ASN][1000 genomes]
rs72707653	0.82[EUR][1000 genomes]
rs7515690	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7552922	0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap]

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	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv872543	chr1:170171083-170674903	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv533915	chr1:170258766-170725296	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12747498	OBP2A	trans	cerebellum	SCAN
rs12747498	GORAB	cis	Artery Tibial	GTEx
rs12747498	SCYL3	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170439400-170441400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:170439400-170441600	Enhancers	Osteobl	bone
3	chr1:170440000-170440400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:170440000-170440800	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr1:170440000-170441200	Enhancers	NHDF-Ad	bronchial
6	chr1:170440000-170441600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:170440200-170440400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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