Variant report

Variant	rs11924101
Chromosome Location	chr3:133394478-133394479
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1006098	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10935071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497433	1.00[CEU][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12497513	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]
rs1444597	0.82[AMR][1000 genomes]
rs1822744	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1867503	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1867504	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1867505	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2589269	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3772680	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4854736	0.83[EUR][1000 genomes]
rs4854737	0.91[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11924101	TOPBP1	cis	cerebellum	SCAN
rs11924101	SOX14	cis	parietal	SCAN
rs11924101	TOPBP1	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133389400-133394600	Enhancers	HepG2	liver
2	chr3:133393200-133395800	Enhancers	GM12878-XiMat	blood
3	chr3:133393600-133395000	Enhancers	Liver	Liver
4	chr3:133393600-133395200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
5	chr3:133393800-133395400	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:133393800-133395800	Enhancers	Adipose Nuclei	Adipose
7	chr3:133393800-133396200	Weak transcription	Right Atrium	heart
8	chr3:133393800-133406800	Weak transcription	Brain Substantia Nigra	brain
9	chr3:133394000-133394800	Weak transcription	Brain Angular Gyrus	brain
10	chr3:133394000-133395400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
11	chr3:133394000-133399600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:133394200-133395600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:133394200-133395600	Enhancers	Pancreas	Pancrea
14	chr3:133394400-133394600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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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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