Variant report

Variant	rs6097809
Chromosome Location	chr20:52773510-52773511
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12624824	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2045844	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6022979	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6091821	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6091822	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6097777	0.83[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs6097779	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6097789	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6097795	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6123360	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6127114	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62214478	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62214479	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62214503	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8117026	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8120563	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8124440	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8124792	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv1063981	chr20:52765317-52776613	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2762085	chr20:52765329-52776625	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv1058882	chr20:52765979-52794372	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6097809	SCGB2A2	trans	brain	seeQTL
rs6097809	SCGB1D2	trans	brain	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52768800-52790200	Transcr. at gene 5' and 3'	A549	lung
2	chr20:52769200-52789400	Weak transcription	Esophagus	oesophagus
3	chr20:52769600-52785800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:52769800-52777600	Weak transcription	HepG2	liver
5	chr20:52771200-52779000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr20:52771200-52786000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr20:52773000-52773600	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr20:52773400-52773600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
9	chr20:52773400-52774800	Weak transcription	Brain Germinal Matrix	brain

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links