Variant report

Variant	rs12562202
Chromosome Location	chr1:217102472-217102473
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1030854	0.85[JPT][hapmap]
rs10492959	0.85[JPT][hapmap]
rs10863284	0.88[JPT][hapmap]
rs11117734	0.84[JPT][hapmap]
rs2099557	0.82[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2576199	0.85[JPT][hapmap]
rs2818758	0.85[JPT][hapmap]
rs6678414	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.94[ASN][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	nsv873179	chr1:217056893-217112871	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv873180	chr1:217073060-217112871	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv520457	chr1:217102061-217102472	Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12562202	LPGAT1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:217088800-217112000	Weak transcription	Pancreas	Pancrea
2	chr1:217093400-217104800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:217097000-217102800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:217101000-217102600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:217101000-217103000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:217101000-217103600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:217101200-217109600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:217101800-217102600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:217101800-217103200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:217102000-217107200	Weak transcription	Fetal Intestine Small	intestine

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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