Variant report

Variant	rs1003641
Chromosome Location	chr11:113273636-113273637
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1076560	0.81[CHD][hapmap]
rs1076562	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs1079595	0.83[CHB][hapmap]
rs10891545	0.87[CHD][hapmap];0.83[JPT][hapmap]
rs11214598	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11214601	0.83[CHB][hapmap]
rs11214602	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1124491	0.83[CHB][hapmap]
rs1124492	0.89[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1124493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12224538	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs1800497	0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs2002453	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs2005313	0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2242592	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2245805	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs2471856	0.88[ASN][1000 genomes]
rs2511521	0.92[ASN][1000 genomes]
rs2587550	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587552	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2734841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2734842	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2859543	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859544	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859545	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4586205	0.86[JPT][hapmap]
rs4590907	0.88[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs4938014	0.89[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs4938016	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]
rs61492892	0.83[ASN][1000 genomes]
rs6275	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6276	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6278	0.83[CHB][hapmap];0.91[CHD][hapmap]
rs6279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7118900	0.89[CHD][hapmap]
rs7122228	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1003641	TTC12	cis	lesional skin	skin_eQTL
rs1003641	TTC12	cis	Heart Left Ventricle	GTEx
rs1003641	TTC12	cis	parietal	SCAN
rs1003641	SIK3	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:113258800-113287400	Weak transcription	Gastric	stomach
2	chr11:113259200-113276000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:113270600-113275200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:113272400-113275800	Weak transcription	Esophagus	oesophagus
5	chr11:113273000-113275200	Weak transcription	NHEK	skin
6	chr11:113273000-113275400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:113273000-113277600	Weak transcription	Right Ventricle	heart
8	chr11:113273200-113275200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:113273400-113275200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:113273400-113275200	Weak transcription	HMEC	breast
11	chr11:113273600-113274600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:113273600-113275200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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