Variant report

Variant	rs653872
Chromosome Location	chr6:56283552-56283553
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs635177	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs645774	1.00[ASN][1000 genomes]
rs648096	0.81[AFR][1000 genomes]
rs648630	0.94[AFR][1000 genomes]
rs650938	0.81[AFR][1000 genomes]
rs664992	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs679020	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs686202	1.00[ASN][1000 genomes]
rs7775609	0.83[AFR][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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1022577	chr6:56263674-56289698	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs653872	GSTA4	cis	cerebellum	SCAN
rs653872	TGFB1I1	trans	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56271400-56284000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:56281000-56283800	Weak transcription	Fetal Lung	lung
3	chr6:56281400-56283800	Weak transcription	Fetal Stomach	stomach
4	chr6:56281800-56285000	Weak transcription	Osteobl	bone
5	chr6:56282400-56284000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:56283200-56283600	Weak transcription	NHDF-Ad	bronchial

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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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