Variant report

Variant	rs11204408
Chromosome Location	chr17:19577018-19577019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19550468..19552548-chr17:19574981..19577039,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000072210	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11871420	0.82[EUR][1000 genomes]
rs12150145	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2108971	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2165895	0.80[EUR][1000 genomes]
rs2245639	0.80[EUR][1000 genomes]
rs2386143	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2386145	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2453586	0.81[EUR][1000 genomes]
rs2453600	0.82[EUR][1000 genomes]
rs2453601	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28495827	0.83[EUR][1000 genomes]
rs3760489	0.84[EUR][1000 genomes]
rs4925036	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62065943	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62065946	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6587201	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7210433	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7215	0.84[EUR][1000 genomes]
rs7216	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8069478	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8069576	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8074500	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8079648	0.82[EUR][1000 genomes]
rs962800	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9889632	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9903027	0.82[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11204408	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19553200-19577400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr17:19553200-19580000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr17:19555000-19581800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr17:19555000-19582800	Weak transcription	HUVEC	blood vessel
5	chr17:19555600-19578600	Weak transcription	Small Intestine	intestine
6	chr17:19558400-19579200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr17:19559600-19578600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:19559800-19577200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr17:19564000-19581000	Weak transcription	Thymus	Thymus
10	chr17:19567600-19578600	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr17:19567600-19584800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr17:19567800-19578600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr17:19568400-19581800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr17:19568600-19606800	Weak transcription	Psoas Muscle	Psoas
15	chr17:19569000-19582000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr17:19569600-19578600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr17:19569600-19579000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr17:19569600-19584000	Weak transcription	Placenta	Placenta
19	chr17:19569800-19578600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr17:19569800-19578600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr17:19569800-19591000	Weak transcription	Fetal Brain Male	brain
22	chr17:19570000-19578800	Weak transcription	Colonic Mucosa	Colon
23	chr17:19570000-19579200	Weak transcription	Aorta	Aorta
24	chr17:19572600-19582800	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr17:19572800-19580600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr17:19572800-19583000	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr17:19574200-19577200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr17:19574200-19577800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr17:19574200-19579000	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr17:19574200-19580600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr17:19574200-19582400	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr17:19574400-19577400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
33	chr17:19574400-19578600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr17:19574600-19577600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr17:19574600-19579000	Weak transcription	Ovary	ovary
36	chr17:19574800-19577600	Enhancers	Stomach Mucosa	stomach
37	chr17:19574800-19577800	Strong transcription	Spleen	Spleen
38	chr17:19574800-19583600	Weak transcription	GM12878-XiMat	blood
39	chr17:19575000-19577200	Enhancers	HepG2	liver
40	chr17:19575000-19579000	Weak transcription	Primary B cells from cord blood	blood
41	chr17:19575000-19590200	Weak transcription	Right Ventricle	heart
42	chr17:19575400-19577400	Weak transcription	Esophagus	oesophagus
43	chr17:19575400-19577400	Enhancers	Fetal Intestine Small	intestine
44	chr17:19575400-19578200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr17:19575400-19579000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr17:19575400-19579000	Weak transcription	Osteobl	bone
47	chr17:19575400-19579200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr17:19575400-19585400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
49	chr17:19575600-19577200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr17:19575600-19577200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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