Variant report

Variant	rs3750744
Chromosome Location	chr10:50354093-50354094
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:50013766..50016503-chr10:50352628..50354357,2	MCF-7	breast:
2	chr10:50351001..50354708-chr10:50363715..50366252,3	K562	blood:
3	chr10:50341037..50342732-chr10:50351584..50354424,2	K562	blood:

Variant related genes	Relation type
ENSG00000172538	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10218854	0.82[CHB][hapmap]
rs11100995	0.96[ASN][1000 genomes]
rs11101001	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs11592541	0.83[CEU][hapmap];0.92[EUR][1000 genomes]
rs11592975	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11594275	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11594452	0.96[ASN][1000 genomes]
rs11597087	0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs11597983	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11598768	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12243520	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17782866	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1806681	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2246796	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2377981	0.96[ASN][1000 genomes]
rs2377982	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2377983	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2377984	0.96[ASN][1000 genomes]
rs4073200	0.96[ASN][1000 genomes]
rs4073201	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073202	0.96[ASN][1000 genomes]
rs41306832	0.96[ASN][1000 genomes]
rs4272720	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4284329	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4838364	0.82[CHB][hapmap]
rs4838445	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs4838455	0.96[ASN][1000 genomes]
rs4838458	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4838464	0.86[ASN][1000 genomes]
rs55687538	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55783415	0.93[ASN][1000 genomes]
rs55890352	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56364323	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56737365	0.96[ASN][1000 genomes]
rs57286767	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59728475	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61060205	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537495	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs7080670	0.82[CHB][hapmap]
rs7081097	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7088006	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7094220	0.82[CHB][hapmap]
rs7094501	0.96[ASN][1000 genomes]
rs7096516	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs7097375	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73302715	0.96[ASN][1000 genomes]
rs73302716	0.96[ASN][1000 genomes]
rs73302780	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73302786	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73304754	0.91[EUR][1000 genomes]
rs7895212	0.93[ASN][1000 genomes]
rs7924204	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][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	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS 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
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3750744	EBNA1BP2	trans	parietal	SCAN
rs3750744	MSMB	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50343000-50357800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:50346200-50354400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr10:50349600-50357200	Weak transcription	HSMM	muscle
4	chr10:50351400-50354400	Enhancers	Fetal Lung	lung
5	chr10:50351400-50354400	Enhancers	Fetal Muscle Leg	muscle
6	chr10:50351600-50354400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr10:50351600-50354400	Enhancers	NHDF-Ad	bronchial
8	chr10:50353400-50354800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr10:50354000-50354200	Bivalent Enhancer	Lung	lung
10	chr10:50354000-50354400	Enhancers	K562	blood

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