Variant report

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52823927..52826251-chr20:52889879..52892276,2	MCF-7	breast:
2	chr20:52891151..52893259-chr21:33433759..33435627,2	MCF-7	breast:
3	chr20:52891210..52894147-chr20:52899496..52901678,2	MCF-7	breast:
4	chr20:52891755..52894002-chr3:64171405..64173308,2	MCF-7	breast:
5	chr20:52891578..52893729-chr20:52943256..52945368,2	MCF-7	breast:
6	chr20:52891487..52895363-chr20:52902222..52905146,4	MCF-7	breast:
7	chr20:52835239..52838782-chr20:52890174..52893182,4	MCF-7	breast:
8	chr20:52891107..52893591-chr20:52960404..52961944,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction
ENSG00000226017	Chromatin interaction

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10485793	0.81[GIH][hapmap]
rs1293132	0.95[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs1298513	0.86[ASN][1000 genomes]
rs1382016	0.89[AFR][1000 genomes]
rs1477730	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2061721	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2616330	0.86[ASN][1000 genomes]
rs292120	0.83[ASN][1000 genomes]
rs292123	0.88[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs292125	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs292126	0.86[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs292132	0.89[ASN][1000 genomes]
rs292139	0.93[ASN][1000 genomes]
rs292141	0.95[ASN][1000 genomes]
rs292143	0.97[ASN][1000 genomes]
rs292144	0.95[ASN][1000 genomes]
rs292146	0.97[ASN][1000 genomes]
rs4811498	0.89[AFR][1000 genomes]
rs6013944	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6023082	0.92[ASN][1000 genomes]
rs6127152	0.91[GIH][hapmap];0.95[TSI][hapmap]

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	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv834011	chr20:52858341-53086042	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv962638	chr20:52883415-52917517	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv178887	chr20:52885413-52894836	Enhancers Weak transcription	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1382015	KCNG1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52890000-52893200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr20:52891800-52892400	Enhancers	Duodenum Mucosa	Duodenum
3	chr20:52891800-52893800	Enhancers	Stomach Mucosa	stomach

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