Variant report

Variant	rs12367002
Chromosome Location	chr12:12148040-12148041
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10743972	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10772521	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10772523	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10845441	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10845442	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10845443	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10845444	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11054584	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11054589	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3983830	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4375516	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7313719	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7315674	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7971902	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7972254	0.92[AMR][1000 genomes];0.96[EUR][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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898804	chr12:12058411-12202173	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv898805	chr12:12119414-12156322	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12367002	PLBD1	cis	parietal	SCAN
rs12367002	HEBP1	cis	lymphoblastoid	seeQTL
rs12367002	CLEC2B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12144600-12151400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:12146800-12161600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:12147600-12150600	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr12:12147800-12148200	Enhancers	Pancreas	Pancrea
5	chr12:12148000-12148200	Flanking Bivalent TSS/Enh	K562	blood
6	chr12:12148000-12148600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
7	chr12:12148000-12148600	Bivalent/Poised TSS	HepG2	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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