Variant report

Variant	rs6443607
Chromosome Location	chr3:178667976-178667977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11711320	0.91[EUR][1000 genomes]
rs11720081	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13092881	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4245914	0.91[EUR][1000 genomes]
rs4279147	0.91[EUR][1000 genomes]
rs4280676	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4315724	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4337680	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4377525	0.89[EUR][1000 genomes]
rs4395442	0.90[EUR][1000 genomes]
rs4417911	0.91[EUR][1000 genomes]
rs4469018	0.88[EUR][1000 genomes]
rs4501160	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4505756	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4522816	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4525914	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4552405	0.91[EUR][1000 genomes]
rs4579062	0.84[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs4607155	0.84[EUR][1000 genomes]
rs4618261	0.80[EUR][1000 genomes]
rs4626139	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4637331	0.89[CEU][hapmap]
rs4955796	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4955802	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955807	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs4955810	0.89[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs56115013	0.91[EUR][1000 genomes]
rs56154408	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6443614	0.91[EUR][1000 genomes]
rs6772028	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs6789706	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790867	0.89[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs6793769	0.91[EUR][1000 genomes]
rs6793893	0.84[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs6794956	0.84[EUR][1000 genomes]
rs6795238	0.84[EUR][1000 genomes]
rs6800015	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs6804084	0.89[CEU][hapmap]
rs7429173	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7612363	0.91[EUR][1000 genomes]
rs7633318	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs7639391	0.89[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs7643052	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651510	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7652668	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7652946	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9831543	0.84[CEU][hapmap]
rs9846511	0.90[EUR][1000 genomes]
rs9860318	0.87[EUR][1000 genomes]
rs9860749	0.88[EUR][1000 genomes]
rs9879637	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9880749	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1010148	chr3:178650949-178691377	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6443607	EIF2B5	cis	parietal	SCAN
rs6443607	ATP11B	cis	parietal	SCAN
rs6443607	KCNMB3	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178658600-178668200	Weak transcription	HSMM	muscle
2	chr3:178666000-178677800	Weak transcription	HSMMtube	muscle
3	chr3:178667600-178668200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:178667600-178668800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast

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