Variant report

Variant	rs9475400
Chromosome Location	chr6:55638258-55638259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs3798843	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs59831864	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1026411	chr6:55372845-55653498	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	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
4	nsv1019228	chr6:55608688-55653498	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9475400	GSTA2	cis	parietal	SCAN
rs9475400	GSTA3	cis	cerebellum	SCAN
rs9475400	DST	cis	lymphoblastoid	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55618200-55672400	Weak transcription	Placenta	Placenta
2	chr6:55625400-55646600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:55634800-55639000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:55636600-55638600	Weak transcription	Fetal Lung	lung
5	chr6:55637200-55639000	Enhancers	Hela-S3	cervix
6	chr6:55637200-55639800	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr6:55638200-55639000	Genic enhancers	Fetal Heart	heart

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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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