Variant report

Variant	rs6082819
Chromosome Location	chr20:22749135-22749136
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10735149	0.89[EUR][1000 genomes]
rs11697574	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11699126	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11699192	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11906177	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11906209	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11906222	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11906944	0.80[ASN][1000 genomes]
rs13042234	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13043348	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16984461	0.80[ASN][1000 genomes]
rs17681000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17681083	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2103766	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2143903	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2143904	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2179857	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2179858	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2207169	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2404492	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34023416	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35049078	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35465115	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4414746	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55650525	0.80[ASN][1000 genomes]
rs6075949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6075950	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6075951	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6075953	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6075954	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6075955	0.80[ASN][1000 genomes]
rs6075956	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6075962	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6075964	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6075965	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6082815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6082816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6082817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6082818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6082822	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6082825	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6082827	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6082828	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6082829	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6082830	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6082832	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6082833	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6082836	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6082837	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082838	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082839	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082840	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082842	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7274509	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7274843	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7353078	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73900571	0.84[ASN][1000 genomes]
rs8116991	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8119685	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8122403	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8122474	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8123509	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs926744	0.98[EUR][1000 genomes];0.96[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	nsv1061382	chr20:22706041-22763200	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	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
3	nsv528221	chr20:22732749-22767280	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6082819	RALGAPA2	cis	cerebellum	SCAN
rs6082819	C20orf79	cis	cerebellum	SCAN
rs6082819	CST8	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22743200-22751400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr20:22744600-22749200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr20:22745200-22749400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr20:22745400-22750800	Weak transcription	Hela-S3	cervix
5	chr20:22745400-22752400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr20:22745400-22752400	Weak transcription	Gastric	stomach
7	chr20:22745800-22749400	Weak transcription	Stomach Mucosa	stomach
8	chr20:22746000-22749200	Weak transcription	NHEK	skin
9	chr20:22746000-22749400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr20:22746000-22751000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr20:22746000-22756000	Weak transcription	Spleen	Spleen
12	chr20:22747800-22751400	Enhancers	Placenta	Placenta
13	chr20:22748000-22749600	Enhancers	Placenta Amnion	Placenta Amnion
14	chr20:22748200-22750400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr20:22748600-22750400	Enhancers	HSMM	muscle
16	chr20:22748800-22749400	Enhancers	A549	lung
17	chr20:22748800-22749600	Enhancers	Fetal Muscle Leg	muscle
18	chr20:22748800-22749800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr20:22748800-22750200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr20:22748800-22750400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr20:22748800-22750400	Enhancers	NHDF-Ad	bronchial
22	chr20:22748800-22751600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr20:22749000-22749200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr20:22749000-22749600	Enhancers	Ovary	ovary
25	chr20:22749000-22749600	Enhancers	NH-A	brain
26	chr20:22749000-22749800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr20:22749000-22749800	Enhancers	HSMMtube	muscle
28	chr20:22749000-22750200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr20:22749000-22752000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr20:22749000-22752200	Enhancers	HMEC	breast

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