Variant report

Variant	rs1004490
Chromosome Location	chr17:19555725-19555726
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr17:19555169-19556316	MCF10A-Er-Src	breast:	n/a	chr17:19555328-19555340 chr17:19555330-19555338 chr17:19555329-19555339
2	FOS	chr17:19555045-19556263	MCF10A-Er-Src	breast:	n/a	chr17:19555328-19555340 chr17:19555330-19555338 chr17:19555329-19555339
3	MYC	chr17:19554917-19556211	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr17:19555168-19556317	MCF10A-Er-Src	breast:	n/a	chr17:19555328-19555340 chr17:19555330-19555338 chr17:19555329-19555339

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19553955..19556054-chr17:19560448..19564216,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264932	TF binding region
ALDH3A2	TF binding region
ENSG00000072210	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1004491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1034897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12601634	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12604069	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12940877	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12945345	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16960251	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2072332	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2120271	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28672254	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2891951	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35364675	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3752046	0.82[EUR][1000 genomes]
rs3786038	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4244600	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4621031	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4646793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646800	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4924788	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4924791	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4925001	0.81[EUR][1000 genomes]
rs4925002	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4925026	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4925037	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925038	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925040	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4925041	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56262978	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58835440	0.82[EUR][1000 genomes]
rs58970893	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61631401	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67870359	0.83[EUR][1000 genomes]
rs68066777	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7216938	0.81[EUR][1000 genomes]
rs73981559	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7502080	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs962801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968012	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9902636	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9909886	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9914765	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv2757654	chr17:19485735-19563766	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	esv2758679	chr17:19485735-19563766	Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv934250	chr17:19551657-19561421	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv933216	chr17:19555486-19561421	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1004490	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL
rs1004490	ALDH3A2	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19552600-19556400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr17:19552800-19557600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:19552800-19557800	Weak transcription	Placenta	Placenta
4	chr17:19553200-19556000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr17:19553200-19556000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr17:19553200-19556600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr17:19553200-19556800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr17:19553200-19557800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr17:19553200-19558200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr17:19553200-19558200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr17:19553200-19558400	Weak transcription	Primary T cells from cord blood	blood
12	chr17:19553200-19566800	Weak transcription	Primary B cells from cord blood	blood
13	chr17:19553200-19577400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr17:19553200-19580000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr17:19553400-19555800	Enhancers	Brain Cingulate Gyrus	brain
16	chr17:19553400-19555800	Enhancers	Fetal Heart	heart
17	chr17:19553400-19556000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr17:19553400-19556200	Enhancers	Fetal Lung	lung
19	chr17:19553400-19556400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr17:19553400-19556800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr17:19553400-19556800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr17:19553400-19558200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr17:19553400-19566400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr17:19553600-19555800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr17:19553600-19556400	Enhancers	Osteobl	bone
26	chr17:19553600-19557600	Weak transcription	Ovary	ovary
27	chr17:19553800-19555800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr17:19553800-19556000	Enhancers	Colon Smooth Muscle	Colon
29	chr17:19553800-19556000	Enhancers	Pancreas	Pancrea
30	chr17:19553800-19556000	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr17:19553800-19556200	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr17:19553800-19556600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr17:19553800-19556800	Weak transcription	Spleen	Spleen
34	chr17:19553800-19560000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr17:19554000-19555800	Flanking Active TSS	Liver	Liver
36	chr17:19554000-19555800	Flanking Active TSS	NHEK	skin
37	chr17:19554000-19556000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr17:19554000-19556200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr17:19554000-19556200	Transcr. at gene 5' and 3'	A549	lung
40	chr17:19554200-19555800	Enhancers	Fetal Intestine Large	intestine
41	chr17:19554200-19556400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr17:19554400-19555800	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr17:19554400-19555800	Flanking Active TSS	HMEC	breast
44	chr17:19554400-19555800	Genic enhancers	Monocytes-CD14+_RO01746	blood
45	chr17:19554400-19556400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr17:19554400-19559400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
47	chr17:19554600-19555800	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr17:19554600-19556200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr17:19554600-19556200	Enhancers	Fetal Intestine Small	intestine
50	chr17:19554600-19557000	Enhancers	Stomach Mucosa	stomach

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