Variant report

Variant	rs6802765
Chromosome Location	chr3:99954721-99954722
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99945013..99946711-chr3:99953102..99955123,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1036770	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10936157	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11915985	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1214369	0.84[EUR][1000 genomes]
rs1214372	0.88[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs1214373	0.88[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs12696084	0.83[CEU][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs13070392	0.88[CEU][hapmap]
rs1609481	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2028494	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2029162	0.95[CHB][hapmap]
rs277636	0.88[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs277637	0.95[CHB][hapmap]
rs277652	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs277654	0.87[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs277655	0.95[CHB][hapmap];0.91[CHD][hapmap]
rs34547730	0.85[ASN][1000 genomes]
rs35939236	0.83[ASN][1000 genomes]
rs3772698	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4552390	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4928118	0.95[CHB][hapmap]
rs4928119	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4928169	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62281675	0.88[EUR][1000 genomes]
rs6763594	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6804963	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs6808175	0.87[EUR][1000 genomes]
rs7427443	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7618677	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs7630257	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7637157	0.88[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs7638503	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs931332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs967608	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9863738	0.88[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs9880795	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs9882337	0.87[EUR][1000 genomes]
rs9968163	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS 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	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6802765	ZNF546	trans	parietal	SCAN
rs6802765	TBC1D23	cis	Muscle Skeletal	GTEx
rs6802765	ZPLD1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99946400-99956600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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