Variant report

Variant	rs6082843
Chromosome Location	chr20:22778715-22778716
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:22774202..22776469-chr20:22777682..22779522,2	MCF-7	breast:
2	chr20:22778208..22779961-chr20:22785655..22787174,2	MCF-7	breast:
3	chr20:22776919..22778852-chr20:22779074..22780596,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1997880	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2424463	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2424467	0.81[EUR][1000 genomes]
rs2424471	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2424472	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2424474	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2424477	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2424478	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4813469	0.84[AMR][1000 genomes]
rs4815142	0.80[EUR][1000 genomes]
rs6048344	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6082809	0.82[AMR][1000 genomes]
rs6113805	0.81[EUR][1000 genomes]
rs6132546	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs932466	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6082843	GINS1	cis	cerebellum	SCAN
rs6082843	ZNF337	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22774800-22778800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr20:22774800-22779000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr20:22774800-22779000	Enhancers	NHEK	skin
4	chr20:22776400-22779800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr20:22776400-22780800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr20:22776400-22785800	Weak transcription	Right Atrium	heart
7	chr20:22776600-22781400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr20:22776600-22781400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr20:22777000-22781400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr20:22777400-22782400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr20:22777600-22780000	Weak transcription	HSMMtube	muscle
12	chr20:22777600-22781000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr20:22777600-22782800	Weak transcription	Aorta	Aorta
14	chr20:22778000-22778800	Enhancers	Lung	lung
15	chr20:22778200-22780400	Weak transcription	A549	lung
16	chr20:22778200-22780400	Weak transcription	HSMM	muscle
17	chr20:22778200-22782000	Weak transcription	NHLF	lung
18	chr20:22778400-22778800	Enhancers	Placenta	Placenta
19	chr20:22778400-22782000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr20:22778600-22779200	Weak transcription	Spleen	Spleen
21	chr20:22778600-22780400	Weak transcription	Fetal Muscle Leg	muscle
22	chr20:22778600-22780800	Weak transcription	HMEC	breast
23	chr20:22778600-22781400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr20:22778600-22782800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr20:22778600-22786200	Weak transcription	Gastric	stomach

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