Variant report

Variant	rs6580695
Chromosome Location	chr12:49201207-49201208
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10875876	0.97[ASN][1000 genomes]
rs10875877	0.99[ASN][1000 genomes]
rs1532365	0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2070615	0.85[CEU][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2446989	0.99[ASN][1000 genomes]
rs2446992	0.99[ASN][1000 genomes]
rs2453468	0.91[ASN][1000 genomes]
rs2453469	0.85[JPT][hapmap]
rs2453478	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2453479	0.99[ASN][1000 genomes]
rs2860360	0.91[ASN][1000 genomes]
rs2926803	0.99[ASN][1000 genomes]
rs2926804	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs3101344	0.98[ASN][1000 genomes]
rs4760643	0.99[ASN][1000 genomes]
rs903568	0.87[ASN][1000 genomes]
rs931570	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9706255	0.82[CHB][hapmap]

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	nsv826363	chr12:49177227-49250989	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6580695	PLEKHA9	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49190400-49204000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:49195200-49204200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:49196000-49204000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:49198000-49204400	Weak transcription	Lung	lung
5	chr12:49199000-49204400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:49199400-49203800	Weak transcription	NHLF	lung
7	chr12:49199400-49204000	Weak transcription	Fetal Intestine Small	intestine
8	chr12:49199600-49201800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:49200400-49201400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr12:49200400-49201400	Enhancers	HepG2	liver
11	chr12:49200400-49201600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:49201200-49207600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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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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