Variant report

Variant	rs13028226
Chromosome Location	chr2:190049780-190049781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190045305..190048072-chr2:190048606..190050123,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10165257	0.92[ASN][1000 genomes]
rs1016622	0.82[AFR][1000 genomes]
rs10166385	0.92[ASN][1000 genomes]
rs10167242	0.84[ASN][1000 genomes]
rs10172607	0.94[ASN][1000 genomes]
rs10173224	0.92[ASN][1000 genomes]
rs10184895	0.94[ASN][1000 genomes]
rs10755002	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10931401	0.94[ASN][1000 genomes]
rs10931403	0.90[ASN][1000 genomes]
rs10931405	0.88[ASN][1000 genomes]
rs10931411	0.82[ASN][1000 genomes]
rs11901914	0.92[ASN][1000 genomes]
rs12474942	0.96[ASN][1000 genomes]
rs12621657	0.84[ASN][1000 genomes]
rs12999125	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13005834	0.80[AFR][1000 genomes]
rs13006065	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs13015183	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13031609	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13408928	0.92[ASN][1000 genomes]
rs13411992	0.92[ASN][1000 genomes]
rs13413518	0.92[ASN][1000 genomes]
rs1356161	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1356165	0.84[AFR][1000 genomes]
rs1356166	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1464135	0.92[ASN][1000 genomes]
rs1474000	0.85[ASN][1000 genomes]
rs1515866	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1533618	0.94[ASN][1000 genomes]
rs1546617	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1913892	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1973666	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1983318	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2351631	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2351632	0.95[ASN][1000 genomes]
rs2351633	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2351635	0.84[ASN][1000 genomes]
rs4667266	0.82[AFR][1000 genomes]
rs4667268	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4667270	0.92[ASN][1000 genomes]
rs4667271	0.94[ASN][1000 genomes]
rs4667275	0.84[ASN][1000 genomes]
rs6434334	0.87[ASN][1000 genomes]
rs6434337	0.83[ASN][1000 genomes]
rs6704568	0.86[ASN][1000 genomes]
rs6728877	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6732534	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6761868	0.86[ASN][1000 genomes]
rs7574281	0.82[ASN][1000 genomes]
rs7599222	0.92[ASN][1000 genomes]
rs7603704	0.89[ASN][1000 genomes]
rs939158	0.84[ASN][1000 genomes]
rs939160	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13028226	AC013439.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190045800-190053000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr2:190045800-190056600	Weak transcription	HSMM	muscle
3	chr2:190046600-190057600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:190049200-190052800	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links