Variant report

Variant	rs601293
Chromosome Location	chr11:75362041-75362042
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:75351036..75353182-chr11:75360194..75362625,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1368135	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2015782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2511005	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs544997	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes]
rs570559	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs581522	0.82[EUR][1000 genomes]
rs584046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs585433	0.82[JPT][hapmap]
rs588955	0.82[JPT][hapmap]
rs589063	0.82[JPT][hapmap]
rs599816	0.82[JPT][hapmap]
rs601142	0.86[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs609131	0.94[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs611221	0.86[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs617449	0.94[CHB][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs61897968	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs629176	0.94[CHB][hapmap];0.82[EUR][1000 genomes]
rs636418	0.82[JPT][hapmap]
rs640277	0.80[EUR][1000 genomes]
rs642002	0.83[CEU][hapmap];0.94[CHB][hapmap];0.83[YRI][hapmap];0.83[EUR][1000 genomes]
rs644388	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs648930	0.86[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs652524	0.94[CHB][hapmap];0.80[EUR][1000 genomes]
rs664133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs678320	0.81[EUR][1000 genomes]
rs678874	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs683195	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs684644	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381903	chr11:75123498-75587233	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs601293	CTD-2530H12.4	cis	Artery Tibial	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75351600-75366600	Weak transcription	Brain Anterior Caudate	brain
2	chr11:75353800-75366400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr11:75355000-75362600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr11:75355000-75366200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr11:75355200-75366400	Weak transcription	Fetal Brain Male	brain
6	chr11:75355400-75362400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr11:75357000-75365200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:75359000-75364200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr11:75361000-75363000	Enhancers	Fetal Heart	heart
10	chr11:75362000-75362200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr11:75362000-75362800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:75362000-75363600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:75362000-75366400	Weak transcription	Fetal Brain Female	brain

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