Variant report

Variant	rs4955439
Chromosome Location	chr3:49245645-49245646
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 35 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10154992	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130183	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130186	0.87[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130187	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11710434	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719762	0.95[CEU][hapmap]
rs11720542	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720657	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs12637346	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13084037	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13096474	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap]
rs2082923	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099526	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs2177268	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs3087866	0.82[MEX][hapmap]
rs3448	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs35713889	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4292260	0.87[CEU][hapmap]
rs4384984	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955411	0.87[CEU][hapmap]
rs4955414	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955416	0.82[CEU][hapmap]
rs4955417	0.95[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4955421	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955423	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955426	0.87[CEU][hapmap]
rs4955427	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955430	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs4955443	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974081	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs56127630	1.00[ASN][1000 genomes]
rs62259933	1.00[ASN][1000 genomes]
rs62259943	1.00[ASN][1000 genomes]
rs62259944	1.00[ASN][1000 genomes]
rs62259947	1.00[ASN][1000 genomes]
rs6446256	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446257	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6769821	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778080	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785045	1.00[ASN][1000 genomes]
rs6787808	0.82[CEU][hapmap]
rs6798112	0.85[CEU][hapmap]
rs6803264	0.80[EUR][1000 genomes]
rs6805609	1.00[ASN][1000 genomes]
rs6808036	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809204	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809851	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7100	0.82[MEX][hapmap]
rs72934271	1.00[ASN][1000 genomes]
rs73088137	1.00[ASN][1000 genomes]
rs7355800	1.00[ASN][1000 genomes]
rs7429661	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7432077	0.86[EUR][1000 genomes]
rs7613491	1.00[ASN][1000 genomes]
rs7617480	1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs7619016	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626076	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631586	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638750	1.00[ASN][1000 genomes]
rs7647973	1.00[ASN][1000 genomes]
rs7648995	1.00[ASN][1000 genomes]
rs8897	1.00[ASN][1000 genomes]
rs9586	1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs974495	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap]
rs9757181	0.95[CEU][hapmap]
rs9817807	1.00[ASN][1000 genomes]
rs9831648	1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs9834003	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842132	1.00[ASN][1000 genomes]
rs9860055	1.00[ASN][1000 genomes]
rs9860285	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9865051	0.87[CEU][hapmap];0.82[TSI][hapmap]
rs9867285	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881860	0.95[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:35)

SNP	Gene	Cis/trans	Tissue	Source
rs4955439	ARIH2	cis	Thyroid	GTEx
rs4955439	WDR6	cis	Nerve Tibial	GTEx
rs4955439	P4HTM	cis	parietal	SCAN
rs4955439	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs4955439	AMT	cis	Thyroid	GTEx
rs4955439	DALRD3	cis	cerebellum	SCAN
rs4955439	ZNF589	cis	parietal	SCAN
rs4955439	GPX1	cis	parietal	SCAN
rs4955439	AMT	cis	multi-tissue	Pritchard
rs4955439	WDR6	cis	parietal	SCAN
rs4955439	AMT	cis	Esophagus Muscularis	GTEx
rs4955439	AMT	cis	Esophagus Mucosa	GTEx
rs4955439	SEMA3G	cis	cerebellum	SCAN
rs4955439	AMT	cis	Nerve Tibial	GTEx
rs4955439	WDR6	cis	multi-tissue	Pritchard
rs4955439	NICN1	cis	cerebellum	SCAN
rs4955439	MST1R	cis	multi-tissue	Pritchard
rs4955439	AMT	cis	lymphoblastoid	seeQTL
rs4955439	NICN1	cis	multi-tissue	Pritchard
rs4955439	AMT	cis	parietal	SCAN
rs4955439	NCKIPSD	cis	multi-tissue	Pritchard
rs4955439	WDR6	cis	cerebellum	SCAN
rs4955439	AMT	cis	lung	GTEx
rs4955439	NICN1	cis	Thyroid	GTEx
rs4955439	AMT	cis	Muscle Skeletal	GTEx
rs4955439	NICN1-AS1	cis	Thyroid	GTEx
rs4955439	DALRD3	cis	parietal	SCAN
rs4955439	WDR6	cis	Muscle Skeletal	GTEx
rs4955439	QRICH1	cis	cerebellum	SCAN
rs4955439	GMPPB	cis	parietal	SCAN
rs4955439	AMT	cis	Adipose Subcutaneous	GTEx
rs4955439	AMT	cis	Artery Tibial	GTEx
rs4955439	AMT	cis	Artery Aorta	GTEx
rs4955439	AMT	cis	Whole Blood	GTEx
rs4955439	AMT	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49237600-49255600	Weak transcription	Left Ventricle	heart
2	chr3:49237800-49248400	Weak transcription	Fetal Stomach	stomach
3	chr3:49237800-49251000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:49237800-49251200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:49238200-49248600	Weak transcription	Osteobl	bone
6	chr3:49238200-49249800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:49238200-49251000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:49238200-49251000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:49238200-49251000	Weak transcription	NHLF	lung
10	chr3:49238200-49255400	Weak transcription	Right Ventricle	heart
11	chr3:49239400-49251000	Weak transcription	Ovary	ovary
12	chr3:49243200-49249600	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:49243200-49255200	Weak transcription	Fetal Heart	heart
14	chr3:49243400-49251200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:49244200-49246000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:49245400-49246800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:49245600-49245800	Enhancers	Right Atrium	heart
18	chr3:49245600-49246200	Enhancers	Adipose Nuclei	Adipose
19	chr3:49245600-49246400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:49245600-49247000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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