Variant report

Variant	rs4961497
Chromosome Location	chr9:16797461-16797462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10962594	0.90[CEU][hapmap];0.91[GIH][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs10962598	0.91[GIH][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs10962601	0.85[JPT][hapmap]
rs10962604	0.87[CHB][hapmap];0.80[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10962606	0.87[CHB][hapmap];0.80[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10962608	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16935071	0.94[EUR][1000 genomes]
rs2253579	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs34926199	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs57542309	0.94[EUR][1000 genomes]
rs7861010	0.86[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2758627	chr9:16641966-16809203	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2759673	chr9:16641966-16809203	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv892650	chr9:16696187-16950860	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv613671	chr9:16792350-16804082	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4961497	PLIN2	cis	cerebellum	SCAN
rs4961497	SH3GL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16784400-16802200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr9:16787200-16797600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:16788200-16798000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr9:16794600-16799000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr9:16794600-16799200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr9:16794800-16799000	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr9:16794800-16799800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:16795000-16798000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr9:16795000-16799200	Enhancers	Rectal Smooth Muscle	rectum
10	chr9:16795200-16798000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:16795600-16797600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:16796200-16798800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:16796200-16799000	Enhancers	NHDF-Ad	bronchial
14	chr9:16796200-16801400	Weak transcription	Fetal Stomach	stomach
15	chr9:16796200-16801400	Weak transcription	Ovary	ovary
16	chr9:16796200-16801400	Weak transcription	NHLF	lung
17	chr9:16796200-16803800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:16796200-16810400	Weak transcription	HSMM	muscle
19	chr9:16796200-16813400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr9:16796200-16816800	Weak transcription	HSMMtube	muscle
21	chr9:16796400-16797800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr9:16796400-16802200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr9:16796400-16824400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr9:16796600-16797600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:16796600-16797800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr9:16796600-16802200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr9:16796600-16809000	Weak transcription	Osteobl	bone
28	chr9:16797000-16798000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr9:16797200-16798000	Enhancers	H1 Cell Line	embryonic stem cell
30	chr9:16797400-16798000	Enhancers	H9 Cell Line	embryonic stem cell
31	chr9:16797400-16798200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:16797400-16799200	Enhancers	Colon Smooth Muscle	Colon

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