Variant report

Variant	rs1340043
Chromosome Location	chr9:18458068-18458069
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10756963	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10756964	0.95[ASN][1000 genomes]
rs10810969	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10810970	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10810971	0.95[ASN][1000 genomes]
rs10963613	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1281350	0.83[CHB][hapmap];0.81[LWK][hapmap]
rs1329720	1.00[CEU][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1329721	0.88[ASN][1000 genomes]
rs1340039	0.87[ASN][1000 genomes]
rs1340040	0.88[ASN][1000 genomes]
rs1340042	0.94[ASN][1000 genomes]
rs1341063	1.00[CEU][hapmap];0.82[CHD][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1417035	0.90[ASN][1000 genomes]
rs1576383	0.93[ASN][1000 genomes]
rs16936779	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1832747	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1888067	0.82[CHD][hapmap]
rs1999174	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2000047	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2153414	0.90[ASN][1000 genomes]
rs2153415	0.82[JPT][hapmap]
rs2153416	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs4961652	0.83[JPT][hapmap]
rs6475216	0.90[ASN][1000 genomes]
rs6475218	0.85[ASN][1000 genomes]
rs7019399	0.83[JPT][hapmap]
rs7032393	0.95[ASN][1000 genomes]
rs7046502	0.95[ASN][1000 genomes]
rs7856703	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs7864622	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs7864727	0.91[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831522	chr9:18231982-18459492	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv892688	chr9:18385143-18551247	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1029449	chr9:18414752-18829127	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv540077	chr9:18414752-18829127	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv1030931	chr9:18414752-18903530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18456600-18458600	Weak transcription	Fetal Intestine Small	intestine
2	chr9:18456800-18458200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr9:18456800-18458800	Enhancers	NHDF-Ad	bronchial
4	chr9:18456800-18459600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:18456800-18459800	Enhancers	HUVEC	blood vessel
6	chr9:18457000-18459800	Enhancers	NHEK	skin
7	chr9:18457200-18458200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:18457200-18459000	Weak transcription	Fetal Intestine Large	intestine
9	chr9:18457200-18461600	Enhancers	HMEC	breast
10	chr9:18457400-18458200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:18457600-18458200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr9:18457600-18458600	Weak transcription	Hela-S3	cervix
13	chr9:18457600-18460400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:18457800-18459400	Weak transcription	NH-A	brain
15	chr9:18457800-18463800	Weak transcription	NHLF	lung
16	chr9:18458000-18459200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:18458000-18459200	Weak transcription	Osteobl	bone
18	chr9:18458000-18459400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:18458000-18459600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:18458000-18463800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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