Variant report

Variant	rs6036641
Chromosome Location	chr20:24078476-24078477
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1160365	0.87[EUR][1000 genomes]
rs34016617	1.00[EUR][1000 genomes]
rs34096340	0.87[EUR][1000 genomes]
rs34097439	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34123386	0.87[EUR][1000 genomes]
rs35671594	0.87[EUR][1000 genomes]
rs35675087	1.00[EUR][1000 genomes]
rs6036634	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6036639	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6036642	0.97[ASN][1000 genomes]
rs6036643	0.97[ASN][1000 genomes]
rs6036647	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6049376	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6049384	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6049385	0.96[ASN][1000 genomes]
rs6049387	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6049388	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6049391	0.97[ASN][1000 genomes]
rs6049395	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6114474	0.96[ASN][1000 genomes]
rs6132697	1.00[EUR][1000 genomes]
rs6132698	1.00[EUR][1000 genomes]
rs6132699	0.89[EUR][1000 genomes]
rs6132702	0.87[EUR][1000 genomes]
rs6138198	0.97[EUR][1000 genomes]
rs6138199	1.00[EUR][1000 genomes]
rs6138206	0.95[EUR][1000 genomes]
rs6138211	0.87[EUR][1000 genomes]
rs6138213	1.00[CEU][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs62193667	1.00[EUR][1000 genomes]
rs74173629	0.89[EUR][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	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1056491	chr20:23955040-24105080	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6036641	SNORA2A	trans	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24075000-24081000	Enhancers	Placenta Amnion	Placenta Amnion
2	chr20:24076200-24082800	Weak transcription	HMEC	breast
3	chr20:24076600-24079200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr20:24076800-24078800	Enhancers	Placenta	Placenta
5	chr20:24077000-24079200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr20:24077000-24079200	Weak transcription	NHEK	skin
7	chr20:24077200-24079400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr20:24077400-24079400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr20:24077400-24081200	Weak transcription	Pancreas	Pancrea
10	chr20:24077800-24082800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr20:24078000-24079400	Weak transcription	Ovary	ovary
12	chr20:24078000-24081200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr20:24078400-24081000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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