Variant report

Variant	rs4925036
Chromosome Location	chr17:19553659-19553660
allele	A/G
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	chr17:19553530-19553811	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr17:19553539-19553768	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr17:19553546-19553782	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:19549675..19554690-chr17:19558689..19564889,9	MCF-7	breast:
2	chr17:19549832..19553259-chr17:19553309..19555611,4	MCF-7	breast:
3	chr17:19552711..19555521-chr17:19564350..19566731,2	MCF-7	breast:

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

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11204408	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11656199	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11656773	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11871420	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12150145	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12941194	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17684040	0.89[EUR][1000 genomes]
rs1812051	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2108971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120274	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2165895	0.88[EUR][1000 genomes]
rs2245639	0.89[EUR][1000 genomes]
rs2386141	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2386142	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2386143	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386145	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440162	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2453586	0.89[EUR][1000 genomes]
rs2453600	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2453601	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2453604	0.89[EUR][1000 genomes]
rs2453608	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28495827	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28537694	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3760489	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4273101	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs56109259	0.88[EUR][1000 genomes]
rs62065943	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62065946	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6587200	0.86[EUR][1000 genomes]
rs6587201	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7210433	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7215	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7405861	0.84[EUR][1000 genomes]
rs7405862	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7502992	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8069478	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8069576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074500	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8074784	0.82[EUR][1000 genomes]
rs8079648	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8081130	0.81[YRI][hapmap]
rs962800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889632	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9903027	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4925036	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19550200-19555200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr17:19551000-19553800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr17:19551000-19553800	Active TSS	Right Ventricle	heart
4	chr17:19551000-19554600	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr17:19551200-19553800	Active TSS	Brain Angular Gyrus	brain
6	chr17:19551200-19554000	Active TSS	Aorta	Aorta
7	chr17:19551200-19554200	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr17:19551200-19554600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr17:19551200-19554800	Active TSS	Esophagus	oesophagus
10	chr17:19551200-19554800	Active TSS	Right Atrium	heart
11	chr17:19551400-19553800	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr17:19551400-19553800	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr17:19551400-19553800	Active TSS	Fetal Brain Female	brain
14	chr17:19551400-19554000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr17:19551400-19554400	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr17:19551400-19554600	Active TSS	Brain Anterior Caudate	brain
17	chr17:19551600-19553800	Active TSS	HSMMtube	muscle
18	chr17:19551600-19554000	Active TSS	A549	lung
19	chr17:19551600-19554400	Active TSS	Duodenum Mucosa	Duodenum
20	chr17:19551600-19554600	Active TSS	Hela-S3	cervix
21	chr17:19551800-19554000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr17:19551800-19554000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr17:19552600-19554400	Active TSS	HMEC	breast
24	chr17:19552600-19554800	Weak transcription	Small Intestine	intestine
25	chr17:19552600-19555000	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr17:19552600-19556400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr17:19552800-19553800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr17:19552800-19553800	Enhancers	Spleen	Spleen
29	chr17:19552800-19554000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr17:19552800-19554000	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr17:19552800-19554600	Active TSS	HepG2	liver
32	chr17:19552800-19557600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr17:19552800-19557800	Weak transcription	Placenta	Placenta
34	chr17:19553000-19553800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr17:19553000-19553800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr17:19553000-19553800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr17:19553000-19553800	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr17:19553000-19555000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr17:19553000-19555000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr17:19553200-19553800	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr17:19553200-19553800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr17:19553200-19553800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr17:19553200-19553800	Flanking Active TSS	Brain Germinal Matrix	brain
44	chr17:19553200-19553800	Enhancers	Fetal Muscle Leg	muscle
45	chr17:19553200-19554000	Enhancers	Primary T cells fromperipheralblood	blood
46	chr17:19553200-19554000	Weak transcription	Stomach Mucosa	stomach
47	chr17:19553200-19554200	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr17:19553200-19554200	Active TSS	Brain Hippocampus Middle	brain
49	chr17:19553200-19554200	Weak transcription	HSMM	muscle
50	chr17:19553200-19554200	Weak transcription	NH-A	brain

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