Variant report

Variant	rs12470329
Chromosome Location	chr2:12131309-12131310
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10166800	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10189789	0.88[ASN][1000 genomes]
rs10200682	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10210747	0.92[ASN][1000 genomes]
rs12328935	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1530146	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4477888	0.84[ASN][1000 genomes]
rs7565113	0.88[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs7601660	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv580999	chr2:12119686-12134346	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12470329	PDIA6	cis	parietal	SCAN
rs12470329	PDIA6	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:12125400-12134200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:12127000-12135600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:12129800-12135200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:12130000-12134800	Weak transcription	NHDF-Ad	bronchial
5	chr2:12130000-12135000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:12130200-12134200	Weak transcription	Fetal Muscle Leg	muscle
7	chr2:12130400-12131600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr2:12130600-12132400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr2:12130800-12131600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr2:12131000-12131400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:12131200-12131400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

Quick Search:

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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