Variant report

Variant	rs6127152
Chromosome Location	chr20:52872215-52872216
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52852456..52856671-chr20:52869199..52873917,7	MCF-7	breast:
2	chr20:52827870..52830545-chr20:52871348..52873782,2	MCF-7	breast:
3	chr20:52870852..52872943-chr3:64020016..64022874,4	MCF-7	breast:
4	chr20:52841956..52843835-chr20:52870841..52872482,2	MCF-7	breast:
5	chr20:52823499..52826425-chr20:52871011..52873800,2	MCF-7	breast:
6	chr20:52870717..52873614-chr20:52960428..52962256,2	MCF-7	breast:
7	chr1:155055878..155058411-chr20:52870566..52873238,2	MCF-7	breast:
8	chr20:52722574..52724626-chr20:52869342..52872286,2	MCF-7	breast:
9	chr20:52838493..52841252-chr20:52870452..52872363,2	MCF-7	breast:
10	chr20:52830936..52833739-chr20:52871496..52873804,2	MCF-7	breast:
11	chr20:52872209..52873824-chr20:52943616..52946580,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143590	Chromatin interaction
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10485793	0.89[GIH][hapmap];0.81[JPT][hapmap]
rs1293130	0.80[EUR][1000 genomes]
rs1293133	0.80[ASN][1000 genomes]
rs1382015	0.91[GIH][hapmap];0.95[TSI][hapmap]
rs1382016	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1382017	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1477724	0.80[EUR][1000 genomes]
rs1477729	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28512221	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs292123	0.81[GIH][hapmap]
rs292126	0.81[GIH][hapmap]
rs4811498	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4811499	0.81[JPT][hapmap]
rs4811500	0.81[JPT][hapmap]
rs6013944	0.83[GIH][hapmap]
rs6023078	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6091842	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6097869	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6097871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6097884	0.86[EUR][1000 genomes];0.87[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6127152	KCNG1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52870600-52874400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr20:52870800-52874200	Enhancers	Muscle Satellite Cultured Cells	--
3	chr20:52870800-52874400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr20:52871000-52875000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr20:52871000-52875000	Enhancers	HMEC	breast
6	chr20:52871000-52875400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr20:52871200-52874200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr20:52871200-52875000	Enhancers	NHEK	skin
9	chr20:52871400-52874200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr20:52871400-52874400	Enhancers	Hela-S3	cervix
11	chr20:52871400-52874400	Enhancers	Osteobl	bone
12	chr20:52871400-52875000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr20:52871800-52874000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr20:52871800-52874000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr20:52871800-52874200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr20:52872000-52872400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr20:52872000-52874200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr20:52872200-52873000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr20:52872200-52873000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr20:52872200-52874400	Enhancers	NH-A	brain

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