Variant report

Variant	rs6082840
Chromosome Location	chr20:22773103-22773104
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:22772678..22773287-chr20:46083527..46084295,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10735149	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11087397	0.87[ASN][1000 genomes]
rs11697574	0.88[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11699126	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11699192	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11906177	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11906209	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11906222	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11906944	0.93[ASN][1000 genomes]
rs13042234	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13043348	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16984461	0.93[ASN][1000 genomes]
rs17681000	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17681083	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2103766	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2143903	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143904	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2179857	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2179858	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2207169	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404492	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34023416	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35049078	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35465115	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4414746	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55650525	0.93[ASN][1000 genomes]
rs6075949	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6075950	0.94[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6075951	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6075953	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6075954	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6075955	0.93[ASN][1000 genomes]
rs6075956	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6075962	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6075963	0.87[ASN][1000 genomes]
rs6075964	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6075965	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6075966	0.85[ASN][1000 genomes]
rs6082813	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082815	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082816	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082817	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082818	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082819	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082822	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6082825	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6082827	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6082828	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6082829	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6082830	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6082832	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082833	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6082836	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6082837	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6082838	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6082839	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6082841	0.87[ASN][1000 genomes]
rs6082842	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7274509	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7274843	0.94[CEU][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7353078	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73900571	0.89[ASN][1000 genomes]
rs8116991	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8119685	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8122403	0.94[CEU][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8122474	0.94[CEU][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8123509	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs926744	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6082840	C20orf79	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22770400-22775400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr20:22770600-22775800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr20:22771000-22774200	Weak transcription	Aorta	Aorta
4	chr20:22771000-22774200	Weak transcription	Fetal Muscle Leg	muscle
5	chr20:22771000-22775400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr20:22771000-22776000	Weak transcription	Ovary	ovary
7	chr20:22772000-22773200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr20:22772000-22773200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr20:22772000-22773200	Enhancers	A549	lung
10	chr20:22772000-22778600	Enhancers	HMEC	breast
11	chr20:22772200-22773200	Enhancers	NHEK	skin
12	chr20:22772200-22777400	Enhancers	Placenta	Placenta
13	chr20:22772600-22773200	Enhancers	Right Atrium	heart
14	chr20:22772800-22775400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr20:22773000-22774000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr20:22773000-22774800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr20:22773000-22774800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr20:22773000-22775000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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