Variant report

Variant	rs2587552
Chromosome Location	chr11:113271773-113271774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1003641	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1076562	0.92[ASN][1000 genomes]
rs11214598	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11214602	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1124492	0.84[ASN][1000 genomes]
rs1124493	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12224538	0.83[ASN][1000 genomes]
rs1800497	0.87[AFR][1000 genomes]
rs2002453	0.92[ASN][1000 genomes]
rs2005313	0.92[ASN][1000 genomes]
rs2242592	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2245805	0.92[ASN][1000 genomes]
rs2471856	0.88[ASN][1000 genomes]
rs2511521	0.92[ASN][1000 genomes]
rs2587550	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2734841	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2734842	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2859543	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859544	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859545	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4590907	0.83[ASN][1000 genomes]
rs4938014	0.84[ASN][1000 genomes]
rs4938016	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61492892	0.83[ASN][1000 genomes]
rs6275	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6276	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6279	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7122228	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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	nsv556444	chr11:113234432-113383394	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1040152	chr11:113258065-113285916	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv515795	chr11:113266821-113272925	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2587552	TTC12	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:113258000-113272200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:113258800-113287400	Weak transcription	Gastric	stomach
3	chr11:113259200-113276000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:113259400-113272000	Weak transcription	HMEC	breast
5	chr11:113267600-113272400	Weak transcription	Brain Anterior Caudate	brain
6	chr11:113268200-113272000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr11:113268400-113271800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr11:113268800-113272000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr11:113269000-113272200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:113270200-113272400	Weak transcription	Brain Angular Gyrus	brain
11	chr11:113270600-113275200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:113271400-113271800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr11:113271600-113271800	Enhancers	Esophagus	oesophagus
14	chr11:113271600-113273000	Enhancers	Spleen	Spleen

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