Variant report

Variant	rs4938016
Chromosome Location	chr11:113270015-113270016
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1003641	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1076562	0.91[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs10891541	0.80[ASN][1000 genomes]
rs10891542	0.80[ASN][1000 genomes]
rs10891545	0.87[JPT][hapmap]
rs11214598	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11214602	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1124492	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1124493	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12224538	0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs1800497	0.93[YRI][hapmap]
rs2002453	0.91[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs2005313	0.91[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs2242592	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2245805	0.91[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs2276070	0.82[JPT][hapmap]
rs2471856	0.86[ASN][1000 genomes]
rs2511521	0.90[ASN][1000 genomes]
rs2587550	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2587552	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2734841	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2734842	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2859543	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2859544	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2859545	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28712705	0.80[ASN][1000 genomes]
rs4586205	0.82[JPT][hapmap]
rs4590907	0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs4938014	0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs61492892	0.85[ASN][1000 genomes]
rs6275	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6276	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6279	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7118900	0.83[CHB][hapmap]
rs7122228	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs719803	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv556445	chr11:113266821-113270828	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	n/a	n/a	inside rSNPs	n/a
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4938016	TTC12	cis	lesional skin	skin_eQTL
rs4938016	TTC12	cis	Heart Left Ventricle	GTEx

Chromatin state (count:13 , 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	chr11:113264000-113271400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr11:113265800-113270600	Enhancers	Spleen	Spleen
7	chr11:113267600-113272400	Weak transcription	Brain Anterior Caudate	brain
8	chr11:113268200-113272000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr11:113268400-113271800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr11:113268800-113272000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:113269000-113270400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:113269000-113272200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr11:113270000-113270400	Strong transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links