Variant report

Variant	rs745661
Chromosome Location	chr20:22681891-22681892
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:22681185..22683248-chr20:23028456..23031236,2	MCF-7	breast:
2	chr20:22678470..22680900-chr20:22681245..22683866,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178726	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10485634	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10485635	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10485636	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1072709	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1072710	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11087395	0.84[AMR][1000 genomes]
rs11907108	0.84[AMR][1000 genomes]
rs12479587	0.87[AMR][1000 genomes]
rs12480993	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12481000	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12481542	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13036614	0.84[AMR][1000 genomes]
rs13036740	0.84[AMR][1000 genomes]
rs13036763	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13037107	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13037452	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13037517	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13037670	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13037831	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13037887	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13037911	0.90[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13037976	0.84[AMR][1000 genomes]
rs13038194	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13038208	0.87[AMR][1000 genomes]
rs13038520	0.94[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes]
rs13039038	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13039191	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13039411	0.90[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes]
rs13039474	0.90[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13040066	0.85[EUR][1000 genomes]
rs13040538	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13040962	0.95[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13042154	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13042246	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13043823	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13044630	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13044931	0.86[AMR][1000 genomes]
rs13045430	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1983920	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1983921	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1983922	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1983923	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1983924	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2404489	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34675647	0.89[EUR][1000 genomes]
rs4371419	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4514951	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4603850	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6036197	0.90[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6036205	0.84[AMR][1000 genomes]
rs6036206	0.84[AMR][1000 genomes]
rs6048291	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6048298	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6048300	0.86[CEU][hapmap];0.88[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6048302	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6048327	0.84[AMR][1000 genomes]
rs6048328	0.87[AMR][1000 genomes]
rs6075943	0.81[AMR][1000 genomes]
rs6106548	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6113789	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62203753	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7260708	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7260791	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7262725	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7263541	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7263645	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7264150	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7265587	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7265907	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7266066	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7270014	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7270196	0.90[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7270365	0.84[AMR][1000 genomes]
rs7270493	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7270606	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7272556	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8114980	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8117574	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8117625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8117637	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8117659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8117748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8119621	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8125753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8126106	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs965763	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs996070	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs996071	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833943	chr20:22657016-22703454	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs745661	CST3	cis	lymphoblastoid	seeQTL
rs745661	GGTLC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22679000-22682800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr20:22679200-22682000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr20:22680600-22682000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr20:22681000-22682200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr20:22681200-22682000	Weak transcription	NHEK	skin
6	chr20:22681400-22682000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr20:22681800-22683000	ZNF genes & repeats	HMEC	breast

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