Variant report

Variant	rs3760489
Chromosome Location	chr17:19581009-19581010
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19453936..19455810-chr17:19580606..19582489,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11204407	0.92[YRI][hapmap]
rs11204408	0.84[EUR][1000 genomes]
rs11656199	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11656773	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11871420	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12150145	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12941194	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17684040	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2108971	0.89[CEU][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2120274	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2165895	0.86[EUR][1000 genomes]
rs2245639	0.87[EUR][1000 genomes]
rs2386141	0.83[MEX][hapmap]
rs2386143	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2386145	0.89[CEU][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2440162	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2453586	0.87[EUR][1000 genomes]
rs2453600	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2453601	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2453604	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2453608	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28495827	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3786038	0.92[YRI][hapmap]
rs4273101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925036	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56109259	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62065943	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62065946	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6587200	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587201	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7210433	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7215	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7216	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7405861	0.86[EUR][1000 genomes]
rs7405862	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7502992	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8069478	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8069576	0.89[CEU][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8074500	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8074784	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8079648	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs962800	0.89[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9889632	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9903027	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428337	chr17:19340045-19585774	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1061408	chr17:19458185-19613357	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1055361	chr17:19515267-19582503	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	nsv1062485	chr17:19558644-19608008	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3760489	MAP2K3	cis	cerebellum	SCAN
rs3760489	ALDH3A2	cis	cerebellum	SCAN
rs3760489	ALDH3A2	cis	parietal	SCAN
rs3760489	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19555000-19581800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr17:19555000-19582800	Weak transcription	HUVEC	blood vessel
3	chr17:19567600-19584800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr17:19568400-19581800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr17:19568600-19606800	Weak transcription	Psoas Muscle	Psoas
6	chr17:19569000-19582000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr17:19569600-19584000	Weak transcription	Placenta	Placenta
8	chr17:19569800-19591000	Weak transcription	Fetal Brain Male	brain
9	chr17:19572600-19582800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr17:19572800-19583000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr17:19574200-19582400	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr17:19574800-19583600	Weak transcription	GM12878-XiMat	blood
13	chr17:19575000-19590200	Weak transcription	Right Ventricle	heart
14	chr17:19575400-19585400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
15	chr17:19575600-19581800	Weak transcription	Gastric	stomach
16	chr17:19575600-19584000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr17:19575800-19583000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr17:19575800-19584600	Weak transcription	HSMM	muscle
19	chr17:19575800-19586600	Weak transcription	Colon Smooth Muscle	Colon
20	chr17:19576000-19582200	Weak transcription	HSMMtube	muscle
21	chr17:19576000-19584600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr17:19576000-19596200	Weak transcription	Fetal Heart	heart
23	chr17:19576200-19581400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr17:19576200-19582800	Strong transcription	Adipose Nuclei	Adipose
25	chr17:19576200-19584000	Strong transcription	Fetal Muscle Leg	muscle
26	chr17:19576800-19582600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr17:19576800-19583200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:19577200-19583000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
29	chr17:19577200-19585200	Strong transcription	Fetal Brain Female	brain
30	chr17:19577400-19582800	Strong transcription	Esophagus	oesophagus
31	chr17:19577600-19581200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr17:19577600-19581200	Weak transcription	Stomach Mucosa	stomach
33	chr17:19577600-19581800	Strong transcription	HepG2	liver
34	chr17:19577600-19582400	Strong transcription	Brain Hippocampus Middle	brain
35	chr17:19577600-19582800	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr17:19577800-19581200	Strong transcription	Brain Substantia Nigra	brain
37	chr17:19578200-19581400	Strong transcription	Brain Angular Gyrus	brain
38	chr17:19578200-19582200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr17:19578400-19583400	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr17:19578400-19585000	Strong transcription	Stomach Smooth Muscle	stomach
41	chr17:19578600-19581600	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr17:19578600-19581600	Strong transcription	Rectal Smooth Muscle	rectum
43	chr17:19578600-19582000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr17:19578600-19582600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr17:19578600-19582600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr17:19578600-19582600	Strong transcription	Fetal Kidney	kidney
47	chr17:19578600-19582800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr17:19578600-19582800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr17:19578600-19583000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
50	chr17:19578600-19583000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet

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