Variant report

Variant	rs10154992
Chromosome Location	chr3:49276077-49276078
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 33 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11130183	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130186	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130187	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11710434	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719762	1.00[CEU][hapmap]
rs11720542	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720657	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs12637346	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13084037	1.00[ASN][1000 genomes]
rs13096474	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs13322887	1.00[ASN][1000 genomes]
rs1464569	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs2082923	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099526	0.82[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs2177268	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs3448	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs35713889	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4292260	0.81[ASW][hapmap];0.91[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs4384984	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955411	0.81[ASW][hapmap];0.91[CEU][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs4955414	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955416	0.81[ASW][hapmap];0.86[CEU][hapmap];0.84[MEX][hapmap];0.81[YRI][hapmap]
rs4955417	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4955421	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955423	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955426	0.91[CEU][hapmap]
rs4955427	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955430	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4955439	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]
rs4955443	0.94[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];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
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];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446257	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]
rs6446275	1.00[ASN][1000 genomes]
rs6769821	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778080	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785045	1.00[ASN][1000 genomes]
rs6787808	0.86[CEU][hapmap]
rs6798112	0.90[CEU][hapmap]
rs6805609	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs6808036	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809204	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809851	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs72934271	1.00[ASN][1000 genomes]
rs73088137	1.00[ASN][1000 genomes]
rs7355800	1.00[ASN][1000 genomes]
rs7429661	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];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7432077	0.83[EUR][1000 genomes]
rs7613491	1.00[ASN][1000 genomes]
rs7617480	0.87[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7619016	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626076	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];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631586	0.90[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]
rs7651372	1.00[ASN][1000 genomes]
rs8897	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs940045	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs9586	0.81[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs974495	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs9757181	1.00[CEU][hapmap]
rs9817807	1.00[ASN][1000 genomes]
rs9831648	0.81[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs9834003	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842132	1.00[ASN][1000 genomes]
rs9860055	1.00[ASN][1000 genomes]
rs9860285	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9865051	0.91[CEU][hapmap]
rs9867285	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871024	1.00[ASN][1000 genomes]
rs9881860	1.00[CEU][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:33)

SNP	Gene	Cis/trans	Tissue	Source
rs10154992	ARIH2	cis	Thyroid	GTEx
rs10154992	KLHDC8B	cis	multi-tissue	Pritchard
rs10154992	WDR6	cis	parietal	SCAN
rs10154992	DALRD3	cis	cerebellum	SCAN
rs10154992	WDR6	cis	Heart Left Ventricle	GTEx
rs10154992	AMT	cis	lung	GTEx
rs10154992	WDR6	cis	Muscle Skeletal	GTEx
rs10154992	NICN1	cis	Thyroid	GTEx
rs10154992	P4HTM	cis	parietal	SCAN
rs10154992	AMT	cis	Adipose Subcutaneous	GTEx
rs10154992	AMT	cis	parietal	SCAN
rs10154992	WDR6	cis	Nerve Tibial	GTEx
rs10154992	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs10154992	PFKFB4	cis	Nerve Tibial	GTEx
rs10154992	AMT	cis	Muscle Skeletal	GTEx
rs10154992	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs10154992	ZNF589	cis	parietal	SCAN
rs10154992	NICN1-AS1	cis	Thyroid	GTEx
rs10154992	NICN1	cis	cerebellum	SCAN
rs10154992	AMT	cis	cerebellum	SCAN
rs10154992	AMT	cis	Esophagus Mucosa	GTEx
rs10154992	AMT	cis	Artery Tibial	GTEx
rs10154992	AMT	cis	Nerve Tibial	GTEx
rs10154992	QRICH1	cis	cerebellum	SCAN
rs10154992	SEMA3G	cis	cerebellum	SCAN
rs10154992	WDR6	cis	cerebellum	SCAN
rs10154992	AMT	cis	Artery Aorta	GTEx
rs10154992	GPX1	cis	parietal	SCAN
rs10154992	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs10154992	DALRD3	cis	parietal	SCAN
rs10154992	AMT	cis	Whole Blood	GTEx
rs10154992	AMT	cis	Thyroid	GTEx
rs10154992	GMPPB	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49266200-49292600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:49270200-49283000	Weak transcription	Ovary	ovary
3	chr3:49272400-49277000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:49273800-49278400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr3:49274400-49277800	Weak transcription	Osteobl	bone
6	chr3:49274600-49278200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr3:49275400-49276200	ZNF genes & repeats	Aorta	Aorta
8	chr3:49275400-49276200	Strong transcription	Fetal Muscle Leg	muscle
9	chr3:49275400-49276400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:49275400-49276400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:49275400-49276400	Enhancers	HepG2	liver
12	chr3:49275400-49276600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr3:49275400-49276800	Enhancers	HMEC	breast
14	chr3:49275400-49277000	Enhancers	Primary B cells from peripheral blood	blood
15	chr3:49275400-49277000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:49275400-49277000	Enhancers	Rectal Smooth Muscle	rectum
17	chr3:49275400-49277200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:49275400-49277400	Enhancers	Primary B cells from cord blood	blood
19	chr3:49275400-49277400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:49275400-49277600	Enhancers	Primary hematopoietic stem cells	blood
21	chr3:49275400-49278000	Strong transcription	Fetal Stomach	stomach
22	chr3:49275400-49278200	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr3:49275600-49276200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:49275600-49276400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:49275600-49276400	Flanking Active TSS	K562	blood
26	chr3:49275600-49276600	ZNF genes & repeats	Placenta	Placenta
27	chr3:49275800-49276200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:49275800-49276200	Enhancers	Colon Smooth Muscle	Colon
29	chr3:49275800-49276400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:49275800-49276400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:49275800-49276400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:49275800-49276400	Strong transcription	Fetal Muscle Trunk	muscle
33	chr3:49275800-49276400	Enhancers	Pancreas	Pancrea
34	chr3:49275800-49276400	ZNF genes & repeats	GM12878-XiMat	blood
35	chr3:49275800-49276600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr3:49275800-49277000	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr3:49276000-49276200	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr3:49276000-49276200	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr3:49276000-49276200	Enhancers	NHDF-Ad	bronchial
40	chr3:49276000-49276400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:49276000-49276400	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr3:49276000-49276400	Genic enhancers	NHLF	lung
43	chr3:49276000-49276600	Enhancers	Fetal Heart	heart
44	chr3:49276000-49276600	Flanking Active TSS	NHEK	skin
45	chr3:49276000-49276800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:49276000-49277000	Weak transcription	Fetal Intestine Large	intestine
47	chr3:49276000-49282200	Weak transcription	Left Ventricle	heart
48	chr3:49276000-49285000	Weak transcription	Lung	lung

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