Variant report

Variant	rs6132546
Chromosome Location	chr20:22776951-22776952
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:22710759..22713197-chr20:22776694..22778472,2	MCF-7	breast:
2	chr20:22751785..22755071-chr20:22774743..22777587,3	MCF-7	breast:
3	chr20:22776919..22778852-chr20:22779074..22780596,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1997880	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2424462	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2424463	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2424467	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2424471	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2424472	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2424474	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2424477	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2424478	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4813469	0.83[AMR][1000 genomes]
rs4815142	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6048344	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6082809	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6082843	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6113805	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs932466	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[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	nsv544213	chr20:22722740-22791150	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv912816	chr20:22757960-23062927	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv3334	chr20:22773462-22818362	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6132546	CST8	cis	cerebellum	SCAN
rs6132546	SLC24A3	cis	parietal	SCAN
rs6132546	GINS1	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22772000-22778600	Enhancers	HMEC	breast
2	chr20:22772200-22777400	Enhancers	Placenta	Placenta
3	chr20:22774000-22778200	Enhancers	Placenta Amnion	Placenta Amnion
4	chr20:22774200-22778600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr20:22774200-22778600	Enhancers	Fetal Muscle Leg	muscle
6	chr20:22774200-22778600	Enhancers	HUVEC	blood vessel
7	chr20:22774400-22778400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr20:22774600-22777600	Enhancers	Hela-S3	cervix
9	chr20:22774800-22777400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr20:22774800-22777400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr20:22774800-22777800	Enhancers	Fetal Stomach	stomach
12	chr20:22774800-22778800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr20:22774800-22779000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr20:22774800-22779000	Enhancers	NHEK	skin
15	chr20:22775000-22778000	Enhancers	NHDF-Ad	bronchial
16	chr20:22775000-22778200	Enhancers	HSMM	muscle
17	chr20:22775200-22777600	Enhancers	Adipose Nuclei	Adipose
18	chr20:22775200-22778200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr20:22775400-22777800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr20:22775400-22778600	Enhancers	Spleen	Spleen
21	chr20:22775600-22777400	Flanking Active TSS	A549	lung
22	chr20:22776000-22777000	Enhancers	Fetal Kidney	kidney
23	chr20:22776000-22777200	Bivalent Enhancer	HepG2	liver
24	chr20:22776000-22777600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr20:22776000-22777600	Enhancers	Osteobl	bone
26	chr20:22776000-22778600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr20:22776200-22777000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr20:22776200-22777000	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr20:22776200-22777400	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr20:22776200-22777400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr20:22776400-22777000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr20:22776400-22779800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr20:22776400-22780800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr20:22776400-22785800	Weak transcription	Right Atrium	heart
35	chr20:22776600-22777000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr20:22776600-22777000	Weak transcription	Aorta	Aorta
37	chr20:22776600-22777000	Weak transcription	Gastric	stomach
38	chr20:22776600-22777000	Enhancers	NH-A	brain
39	chr20:22776600-22777600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr20:22776600-22777600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr20:22776600-22777600	Enhancers	HSMMtube	muscle
42	chr20:22776600-22778000	Weak transcription	Lung	lung
43	chr20:22776600-22778200	Enhancers	NHLF	lung
44	chr20:22776600-22781400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr20:22776600-22781400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr20:22776800-22777600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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