Variant report

Variant	rs17480505
Chromosome Location	chr2:40099311-40099312
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10188106	0.91[ASN][1000 genomes]
rs11692413	0.98[ASN][1000 genomes]
rs11695763	0.95[ASN][1000 genomes]
rs12475386	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13424439	0.99[ASN][1000 genomes]
rs1541564	0.82[ASN][1000 genomes]
rs1861248	1.00[ASN][1000 genomes]
rs2080296	0.85[ASN][1000 genomes]
rs2192703	0.98[ASN][1000 genomes]
rs2373702	0.85[ASN][1000 genomes]
rs55768815	0.96[ASN][1000 genomes]
rs60399093	0.97[ASN][1000 genomes]
rs62137179	0.95[ASN][1000 genomes]
rs62137180	0.95[ASN][1000 genomes]
rs62137182	0.95[ASN][1000 genomes]
rs62137183	0.97[ASN][1000 genomes]
rs62137185	0.97[ASN][1000 genomes]
rs62137188	0.91[ASN][1000 genomes]
rs62137214	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6732387	0.85[ASN][1000 genomes]
rs7556977	0.96[ASN][1000 genomes]
rs7562741	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs887994	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003593	chr2:40009597-40165666	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535651	chr2:40009597-40165666	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv873891	chr2:40046658-40173905	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv916300	chr2:40079899-40339019	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv430947	chr2:40080723-40141649	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv581496	chr2:40082054-40123904	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1003896	chr2:40094081-40231585	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17480505	PLEKHH2	cis	cerebellum	SCAN
rs17480505	C2orf56	cis	parietal	SCAN
rs17480505	KCNG3	cis	parietal	SCAN
rs17480505	THADA	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40097400-40099400	Enhancers	HSMM	muscle
2	chr2:40097600-40099400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:40098400-40102200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:40098600-40102400	Weak transcription	Brain Anterior Caudate	brain
5	chr2:40098600-40102400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:40098800-40099400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr2:40098800-40099400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:40098800-40101400	Weak transcription	NHLF	lung
9	chr2:40098800-40102000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:40098800-40102400	Weak transcription	Fetal Stomach	stomach
11	chr2:40098800-40102400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:40099000-40099400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:40099000-40102400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:40099000-40102400	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:40099200-40099400	Enhancers	A549	lung
16	chr2:40099200-40099400	Enhancers	HSMMtube	muscle
17	chr2:40099200-40102200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:40099200-40102400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:40099200-40102400	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:40099200-40102400	Weak transcription	HMEC	breast
21	chr2:40099200-40102400	Weak transcription	NH-A	brain
22	chr2:40099200-40102400	Weak transcription	NHEK	skin
23	chr2:40099200-40102400	Weak transcription	Osteobl	bone
24	chr2:40099200-40102600	Weak transcription	NHDF-Ad	bronchial

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