Variant report

Variant	rs3798836
Chromosome Location	chr6:55656259-55656260
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10948955	0.85[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1374551	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1447129	0.90[TSI][hapmap]
rs1470527	0.90[TSI][hapmap]
rs1947135	0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1947136	0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3823038	0.83[TSI][hapmap]
rs6914731	0.85[ASN][1000 genomes]
rs6929620	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7749809	0.90[TSI][hapmap]
rs7750450	0.90[TSI][hapmap]
rs7767441	0.90[TSI][hapmap]
rs9296803	0.85[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9367665	0.89[ASN][1000 genomes]
rs9475428	0.88[TSI][hapmap]
rs966329	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.87[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	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv885909	chr6:55539010-55674338	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv2752670	chr6:55614978-55781605	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv885910	chr6:55628283-55684300	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv603164	chr6:55631762-55674338	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3798836	GSTA2	cis	parietal	SCAN
rs3798836	GSTA3	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55618200-55672400	Weak transcription	Placenta	Placenta
2	chr6:55643200-55659000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:55648200-55657400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:55648400-55658000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:55654800-55657000	Enhancers	Fetal Heart	heart
6	chr6:55655600-55656600	Weak transcription	Left Ventricle	heart
7	chr6:55655800-55657200	Weak transcription	Fetal Lung	lung
8	chr6:55656000-55656400	Weak transcription	Fetal Brain Male	brain
9	chr6:55656200-55657600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:55656200-55667600	Weak transcription	Fetal Muscle Leg	muscle

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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

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