Variant report

Variant	rs9586
Chromosome Location	chr3:49213637-49213638
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49158589..49160627-chr3:49212099..49214336,2	K562	blood:
2	chr3:49210124..49212449-chr3:49213139..49215737,4	K562	blood:
3	chr3:49201068..49204007-chr3:49213052..49215729,2	K562	blood:
4	chr3:49207629..49210061-chr3:49211282..49215140,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172037	Chromatin interaction
ENSG00000185909	Chromatin interaction
ENSG00000177352	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10154992	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]
rs11130183	0.81[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130186	0.81[ASW][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs11130187	1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11710434	1.00[ASN][1000 genomes]
rs11720542	1.00[ASN][1000 genomes]
rs11720657	1.00[ASN][1000 genomes]
rs13084037	0.82[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2082923	1.00[ASN][1000 genomes]
rs2099526	1.00[ASN][1000 genomes]
rs2140270	1.00[ASN][1000 genomes]
rs2177268	1.00[ASN][1000 genomes]
rs3212	0.82[YRI][hapmap]
rs3448	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[ASW][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs4384984	1.00[ASN][1000 genomes]
rs4955411	0.87[ASW][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs4955414	1.00[ASN][1000 genomes]
rs4955416	0.87[ASW][hapmap];0.86[LWK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs4955417	1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap]
rs4955421	0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955423	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955427	1.00[ASN][1000 genomes]
rs4955430	1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs4955439	1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs4955443	1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs4974080	0.82[YRI][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]
rs6446205	0.85[YRI][hapmap]
rs6446256	0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446257	1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6769821	1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs6778080	1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs6779394	0.89[YRI][hapmap]
rs6785045	1.00[ASN][1000 genomes]
rs6805609	1.00[ASN][1000 genomes]
rs6808036	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809204	1.00[ASN][1000 genomes]
rs6809851	1.00[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap]
rs73088137	1.00[ASN][1000 genomes]
rs7429661	1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7432989	0.89[YRI][hapmap]
rs7617480	0.93[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619016	1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs7626076	1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs7631586	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638750	1.00[ASN][1000 genomes]
rs7648995	1.00[ASN][1000 genomes]
rs8897	1.00[ASN][1000 genomes]
rs974495	1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap]
rs9817807	1.00[ASN][1000 genomes]
rs9831648	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834003	0.81[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840050	0.82[YRI][hapmap]
rs9842132	1.00[ASN][1000 genomes]
rs9860285	1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9865051	0.82[TSI][hapmap]
rs9867285	1.00[ASN][1000 genomes]
rs9881860	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:25)

SNP	Gene	Cis/trans	Tissue	Source
rs9586	AMT	cis	parietal	SCAN
rs9586	NICN1-AS1	cis	Thyroid	GTEx
rs9586	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs9586	DALRD3	cis	cerebellum	SCAN
rs9586	NICN1	cis	Thyroid	GTEx
rs9586	AMT	cis	Nerve Tibial	GTEx
rs9586	GNL3	cis	parietal	SCAN
rs9586	P4HTM	cis	parietal	SCAN
rs9586	SEMA3G	cis	cerebellum	SCAN
rs9586	WDR6	cis	Muscle Skeletal	GTEx
rs9586	GNL3	cis	cerebellum	SCAN
rs9586	WDR6	cis	cerebellum	SCAN
rs9586	DALRD3	cis	parietal	SCAN
rs9586	AMT	cis	Thyroid	GTEx
rs9586	AMT	cis	Whole Blood	GTEx
rs9586	WDR6	cis	lung	GTEx
rs9586	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs9586	NICN1	cis	cerebellum	SCAN
rs9586	ZNF589	cis	parietal	SCAN
rs9586	AMT	cis	cerebellum	SCAN
rs9586	WDR6	cis	Heart Left Ventricle	GTEx
rs9586	GPX1	cis	parietal	SCAN
rs9586	WDR6	cis	parietal	SCAN
rs9586	GMPPB	cis	parietal	SCAN
rs9586	QRICH1	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49209600-49213800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:49209800-49215000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:49210400-49213800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:49210800-49214600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:49211000-49215200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:49211200-49213800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:49211200-49214200	Weak transcription	A549	lung
8	chr3:49211200-49214600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr3:49211200-49218800	Weak transcription	Fetal Kidney	kidney
10	chr3:49211200-49224600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:49211400-49213800	Weak transcription	HUVEC	blood vessel
12	chr3:49211400-49214400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:49211400-49214400	Genic enhancers	Left Ventricle	heart
14	chr3:49211400-49215000	Weak transcription	NHDF-Ad	bronchial
15	chr3:49211400-49216000	Weak transcription	Brain Substantia Nigra	brain
16	chr3:49211400-49217600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:49211600-49214000	Strong transcription	Primary T cells from cord blood	blood
18	chr3:49211600-49214000	Strong transcription	Liver	Liver
19	chr3:49211600-49214200	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:49211600-49214400	Strong transcription	Esophagus	oesophagus
21	chr3:49211600-49214800	Strong transcription	Placenta Amnion	Placenta Amnion
22	chr3:49211600-49215200	Genic enhancers	Adipose Nuclei	Adipose
23	chr3:49211800-49213800	Genic enhancers	Ovary	ovary
24	chr3:49211800-49213800	Strong transcription	Pancreas	Pancrea
25	chr3:49211800-49214000	Strong transcription	NHLF	lung
26	chr3:49211800-49214400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:49211800-49214800	Weak transcription	K562	blood
28	chr3:49211800-49215000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:49211800-49215000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:49211800-49215000	Genic enhancers	Right Ventricle	heart
31	chr3:49211800-49216000	Genic enhancers	Fetal Muscle Trunk	muscle
32	chr3:49211800-49216200	Genic enhancers	Fetal Muscle Leg	muscle
33	chr3:49211800-49216600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:49212000-49213800	Weak transcription	HSMM	muscle
35	chr3:49212000-49214000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:49212000-49214200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:49212000-49214200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:49212000-49214400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
39	chr3:49212000-49215200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:49212000-49215400	Weak transcription	Brain Angular Gyrus	brain
41	chr3:49212000-49216200	Weak transcription	Osteobl	bone
42	chr3:49212200-49213800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:49212200-49214000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:49212200-49214000	Strong transcription	Brain Hippocampus Middle	brain
45	chr3:49212200-49214200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:49212200-49214200	Strong transcription	Colon Smooth Muscle	Colon
47	chr3:49212200-49214400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr3:49212200-49214600	Strong transcription	Placenta	Placenta
49	chr3:49212200-49214800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:49212200-49218800	Weak transcription	HepG2	liver

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