Variant report

Variant	rs4646800
Chromosome Location	chr17:19561429-19561430
allele	G/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	E2F4	chr17:19561393-19561619	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr17:19561188-19561436	MCF10A-Er-Src	breast:	n/a	chr17:19561291-19561299

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19549675..19554690-chr17:19558689..19564889,9	MCF-7	breast:
2	chr17:19558329..19562006-chr17:19563141..19565959,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252349	TF binding region
ALDH3A2	TF binding region
ENSG00000072210	Chromatin interaction
ENSG00000252349	Chromatin interaction
ENSG00000264932	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1004490	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1004491	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1034897	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204407	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12601634	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12604069	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12940877	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12945345	0.89[EUR][1000 genomes]
rs16960251	0.91[EUR][1000 genomes]
rs2072332	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2120271	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28672254	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2891951	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35364675	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3786038	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4244600	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4621031	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4646793	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924788	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4924791	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4925002	0.89[EUR][1000 genomes]
rs4925026	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4925037	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925038	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925040	0.85[ASN][1000 genomes]
rs4925041	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56262978	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58970893	0.89[EUR][1000 genomes]
rs61631401	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67870359	0.80[EUR][1000 genomes]
rs68066777	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7216938	0.80[EUR][1000 genomes]
rs73981559	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7502080	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs962801	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs968012	0.93[EUR][1000 genomes]
rs9902636	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9909886	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9914765	0.83[AMR][1000 genomes];0.94[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	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
9	nsv907865	chr17:19558722-19575721	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4646800	ALDH3A2	cis	multi-tissue	Pritchard
rs4646800	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL
rs4646800	ENSG00000072210	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19553200-19566800	Weak transcription	Primary B cells from cord blood	blood
2	chr17:19553200-19577400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr17:19553200-19580000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:19553400-19566400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr17:19554800-19574400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr17:19555000-19563400	Strong transcription	Fetal Stomach	stomach
7	chr17:19555000-19568800	Weak transcription	NH-A	brain
8	chr17:19555000-19581800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr17:19555000-19582800	Weak transcription	HUVEC	blood vessel
10	chr17:19555200-19566400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr17:19555200-19566600	Weak transcription	NHDF-Ad	bronchial
12	chr17:19555200-19569800	Strong transcription	Fetal Muscle Trunk	muscle
13	chr17:19555200-19576400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr17:19555400-19570000	Strong transcription	Fetal Muscle Leg	muscle
15	chr17:19555600-19562200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr17:19555600-19567200	Weak transcription	Right Atrium	heart
17	chr17:19555600-19569800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr17:19555600-19578600	Weak transcription	Small Intestine	intestine
19	chr17:19555800-19561600	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr17:19555800-19562400	Strong transcription	Brain Hippocampus Middle	brain
21	chr17:19556200-19569800	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr17:19556400-19563600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr17:19556600-19562200	Strong transcription	Adipose Nuclei	Adipose
24	chr17:19556600-19569800	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr17:19557200-19569800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr17:19558000-19562200	Strong transcription	Stomach Smooth Muscle	stomach
27	chr17:19558000-19563600	Strong transcription	HMEC	breast
28	chr17:19558200-19562400	Genic enhancers	HepG2	liver
29	chr17:19558200-19568200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr17:19558200-19569400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr17:19558200-19569600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr17:19558200-19569800	Strong transcription	Fetal Intestine Large	intestine
33	chr17:19558400-19566600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr17:19558400-19566800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr17:19558400-19567200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr17:19558400-19571800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr17:19558400-19579200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr17:19558600-19569800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr17:19558800-19566800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr17:19559000-19561800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr17:19559200-19562200	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr17:19559200-19571800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr17:19559200-19574200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr17:19559400-19561600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr17:19559400-19566800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr17:19559400-19575000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr17:19559400-19575400	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr17:19559600-19562000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr17:19559600-19570800	Strong transcription	Brain Anterior Caudate	brain
50	chr17:19559600-19578600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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