Variant report

Variant	rs793497
Chromosome Location	chr3:99505610-99505611
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11719468	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs1287284	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13059754	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1384062	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1610509	0.88[JPT][hapmap]
rs1718235	0.90[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs2638948	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4577503	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4928150	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4928230	0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs704571	0.88[JPT][hapmap]
rs704572	0.92[JPT][hapmap]
rs704574	0.88[JPT][hapmap]
rs7613864	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7650727	0.87[CHD][hapmap];0.94[JPT][hapmap]
rs792831	0.88[JPT][hapmap]
rs792835	0.88[JPT][hapmap]
rs792836	0.88[JPT][hapmap]
rs792837	0.88[JPT][hapmap]
rs793437	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs793439	0.90[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs793443	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs793446	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs793456	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793464	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs793475	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs793476	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs793483	0.88[JPT][hapmap]
rs793485	0.88[JPT][hapmap]
rs793502	0.90[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs796976	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs813218	0.90[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs793497	FILIP1L	Cis_1M	lymphoblastoid	RTeQTL
rs793497	C3orf26	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99492000-99517600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:99494200-99513600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:99496000-99513000	Weak transcription	NHEK	skin
4	chr3:99499400-99509000	Weak transcription	Aorta	Aorta
5	chr3:99501000-99513000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:99501400-99509000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:99502400-99508800	Weak transcription	Adipose Nuclei	Adipose
8	chr3:99502600-99506800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:99502600-99518200	Weak transcription	HSMMtube	muscle
10	chr3:99502800-99507200	Weak transcription	NHLF	lung
11	chr3:99502800-99508200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:99502800-99518400	Weak transcription	NH-A	brain
13	chr3:99503000-99505800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:99503000-99507200	Weak transcription	NHDF-Ad	bronchial
15	chr3:99503600-99509000	Weak transcription	HUVEC	blood vessel
16	chr3:99504600-99513000	Weak transcription	HSMM	muscle
17	chr3:99505200-99507200	Weak transcription	Osteobl	bone
18	chr3:99505400-99507600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:99505600-99505800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:99505600-99505800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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