Variant report

Variant	rs2389786
Chromosome Location	chr1:85306009-85306010
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11161464	0.80[CEU][hapmap];0.86[CHD][hapmap]
rs1325272	0.93[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1409215	0.86[CEU][hapmap]
rs9662096	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs9726895	0.81[EUR][1000 genomes]
rs9727725	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2389786	SPTBN5	trans	multi-tissue	Pritchard
rs2389786	SPTBN5	cis	Liver	GTEx
rs2389786	Contig37946_RC	cis	multi-tissue	Pritchard

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85289400-85330800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr1:85296600-85312800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:85301200-85306200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:85301400-85306200	Weak transcription	Fetal Heart	heart
5	chr1:85301400-85308600	Weak transcription	Stomach Mucosa	stomach
6	chr1:85301600-85306600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:85301600-85307400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:85301600-85307400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:85302000-85306400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:85302400-85306600	Weak transcription	NHEK	skin
11	chr1:85304000-85313200	Weak transcription	Gastric	stomach
12	chr1:85305600-85306800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:85305800-85306800	Enhancers	Muscle Satellite Cultured Cells	--
14	chr1:85305800-85306800	Enhancers	Osteobl	bone
15	chr1:85305800-85313000	Weak transcription	Left Ventricle	heart
16	chr1:85305800-85313000	Weak transcription	Pancreas	Pancrea
17	chr1:85306000-85306200	Enhancers	Stomach Smooth Muscle	stomach
18	chr1:85306000-85306200	Enhancers	HMEC	breast
19	chr1:85306000-85308000	Weak transcription	Liver	Liver

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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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