Variant report

Variant	rs12497513
Chromosome Location	chr3:133388670-133388671
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1006098	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10935071	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11924101	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12497433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637070	0.88[ASN][1000 genomes]
rs1822744	0.83[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1867503	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1867504	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1867505	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2589269	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3772680	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4854736	0.83[EUR][1000 genomes]
rs4854737	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62282416	0.88[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12497513	TOPBP1	cis	parietal	SCAN
rs12497513	SOX14	cis	parietal	SCAN
rs12497513	TOPBP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133381400-133392400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:133381600-133388800	Weak transcription	Gastric	stomach
3	chr3:133382800-133390200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:133382800-133392800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:133383000-133389000	Weak transcription	Fetal Intestine Small	intestine
6	chr3:133383000-133389000	Weak transcription	A549	lung
7	chr3:133386400-133389600	Enhancers	Liver	Liver
8	chr3:133387200-133390000	Enhancers	Pancreas	Pancrea
9	chr3:133387600-133389800	Enhancers	Fetal Intestine Large	intestine
10	chr3:133387800-133389400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:133387800-133393000	Weak transcription	Right Atrium	heart
12	chr3:133388400-133389400	Flanking Active TSS	HepG2	liver

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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