Variant report

Variant	rs1800497
Chromosome Location	chr11:113270828-113270829
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1003641	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]
rs1076560	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs1079594	0.95[CHB][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs1079595	1.00[CHB][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs1079596	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs1079597	0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs1079598	0.91[ASN][1000 genomes]
rs1079727	0.95[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs10891546	0.88[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs11214598	0.88[CHD][hapmap]
rs11214599	0.99[ASN][1000 genomes]
rs11214601	1.00[CHB][hapmap];0.86[JPT][hapmap];0.99[ASN][1000 genomes]
rs1124491	1.00[CHB][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs1124492	0.80[CHD][hapmap]
rs1124493	0.83[CHB][hapmap];0.91[CHD][hapmap]
rs1125393	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs1125394	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs17115439	0.88[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1962262	0.91[ASN][1000 genomes]
rs2075654	0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2242591	0.98[ASN][1000 genomes]
rs2242593	0.99[ASN][1000 genomes]
rs2283265	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2471851	0.86[JPT][hapmap]
rs2471854	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2471855	0.89[ASN][1000 genomes]
rs2471857	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2511520	0.99[ASN][1000 genomes]
rs2587550	0.83[CHB][hapmap];0.91[CHD][hapmap]
rs2587552	0.87[AFR][1000 genomes]
rs2734836	0.91[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2734841	0.83[CHB][hapmap];0.85[YRI][hapmap]
rs2859543	0.86[AFR][1000 genomes]
rs2859545	0.82[CHB][hapmap];0.91[YRI][hapmap]
rs34863235	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4938012	0.82[JPT][hapmap]
rs4938013	0.88[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4938014	0.80[CHD][hapmap]
rs4938015	0.88[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4938016	0.93[YRI][hapmap]
rs6275	0.91[CHD][hapmap]
rs6276	0.83[CHB][hapmap]
rs6278	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs6279	0.83[CHB][hapmap]
rs7103679	0.86[JPT][hapmap]
rs7118900	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7123797	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7350522	0.81[JPT][hapmap]
rs7945132	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs877138	0.80[CHD][hapmap];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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1800497	TTC12	cis	brain	BrainEAC

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	chr11:113264000-113271400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr11:113267600-113272400	Weak transcription	Brain Anterior Caudate	brain
7	chr11:113268200-113272000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr11:113268400-113271800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr11:113268800-113272000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:113269000-113272200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:113270200-113272400	Weak transcription	Brain Angular Gyrus	brain
12	chr11:113270600-113271600	Weak transcription	Spleen	Spleen
13	chr11:113270600-113275200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr11:113270800-113271600	Weak transcription	Esophagus	oesophagus

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