Variant report

Variant	rs10502365
Chromosome Location	chr18:7909131-7909132
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11873831	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12606212	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12606381	0.83[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12607648	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1372061	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2120320	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2165412	0.91[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28854345	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55742047	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55869040	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56082106	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7227767	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7237870	0.94[CEU][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7244035	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73379961	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8082717	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8087211	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9676009	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][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	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv458016	chr18:7488133-7934001	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv576399	chr18:7488133-7934001	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2762810	chr18:7492090-7924728	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10502365	TWSG1	cis	parietal	SCAN
rs10502365	VAPA	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7886800-7914200	Weak transcription	HepG2	liver
2	chr18:7897400-7913200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr18:7898000-7915200	Weak transcription	Fetal Heart	heart
4	chr18:7899000-7916200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr18:7903400-7910200	Weak transcription	Ovary	ovary
6	chr18:7903400-7914800	Weak transcription	Adipose Nuclei	Adipose
7	chr18:7903400-7915200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr18:7903400-7922200	Weak transcription	Right Atrium	heart
9	chr18:7903400-7922200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr18:7905800-7923000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr18:7906200-7910400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr18:7907200-7909400	Enhancers	Psoas Muscle	Psoas
13	chr18:7907600-7910200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr18:7907800-7909200	Enhancers	Fetal Thymus	thymus
15	chr18:7907800-7922200	Weak transcription	Lung	lung
16	chr18:7907800-7926600	Weak transcription	Aorta	Aorta
17	chr18:7908000-7915000	Weak transcription	Colon Smooth Muscle	Colon
18	chr18:7908200-7919000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr18:7908400-7909200	Enhancers	Thymus	Thymus
20	chr18:7908600-7909200	Enhancers	NHEK	skin
21	chr18:7908600-7909400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr18:7908600-7909400	Enhancers	Hela-S3	cervix
23	chr18:7908600-7909400	Enhancers	HMEC	breast
24	chr18:7908800-7909200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr18:7908800-7909200	Enhancers	Placenta	Placenta
26	chr18:7908800-7909200	Transcr. at gene 5' and 3'	A549	lung
27	chr18:7908800-7909400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr18:7908800-7914800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr18:7909000-7909200	Enhancers	Gastric	stomach
30	chr18:7909000-7909200	Enhancers	Left Ventricle	heart
31	chr18:7909000-7909200	Enhancers	Pancreas	Pancrea
32	chr18:7909000-7909200	Enhancers	Skeletal Muscle Female	skeletal muscle

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