Variant report

Variant	rs1481544
Chromosome Location	chr3:99113228-99113229
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs13070933	0.84[CEU][hapmap]
rs1481521	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1481532	0.91[ASN][1000 genomes]
rs1481555	0.81[EUR][1000 genomes]
rs1531729	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1531730	0.90[ASN][1000 genomes]
rs1871789	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2200019	0.94[EUR][1000 genomes]
rs2246153	0.82[EUR][1000 genomes]
rs2246232	0.82[EUR][1000 genomes]
rs2252791	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2464141	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2623343	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2623365	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2700667	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs9758675	0.87[ASN][1000 genomes]
rs9861463	0.81[EUR][1000 genomes]
rs9863565	0.81[EUR][1000 genomes]
rs9866047	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv530026	chr3:98837320-99340537	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv877216	chr3:99065296-99161022	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1481544	OR5AC2	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99105000-99116800	Weak transcription	Aorta	Aorta
2	chr3:99112000-99113600	Enhancers	NHDF-Ad	bronchial
3	chr3:99112000-99114000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:99112200-99114200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:99112600-99113400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:99112600-99113400	Enhancers	Osteobl	bone
7	chr3:99112600-99113800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:99112600-99113800	Enhancers	Fetal Stomach	stomach
9	chr3:99112600-99113800	Enhancers	HMEC	breast
10	chr3:99112600-99115200	Enhancers	NH-A	brain
11	chr3:99112600-99116200	Enhancers	NHLF	lung
12	chr3:99112600-99116400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:99112800-99116200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:99113000-99113600	Weak transcription	HSMMtube	muscle
15	chr3:99113000-99114200	Enhancers	NHEK	skin
16	chr3:99113000-99114600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:99113000-99116000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:99113000-99116000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:99113200-99114000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:99113200-99115400	Enhancers	HSMM	muscle
21	chr3:99113200-99116200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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