Variant report

Variant	rs7212622
Chromosome Location	chr17:19482607-19482608
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	POLR2A	chr17:19482521-19482836	HepG2	liver:	n/a	n/a
2	POLR2A	chr17:19482563-19482728	HepG2	liver:	n/a	n/a
3	POLR2A	chr17:19482391-19483095	HepG2	liver:	n/a	n/a
4	EP300	chr17:19481590-19483255	SK-N-SH	brain:	n/a	chr17:19483098-19483107

Variant related genes	Relation type
ENSG00000228983	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10735	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2120272	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2120273	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2249885	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2440167	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2453594	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2453595	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2453596	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7212622	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL
rs7212622	CTD-2104P17.1	cis	Nerve Tibial	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19457000-19483000	Weak transcription	Psoas Muscle	Psoas
2	chr17:19464000-19483800	Weak transcription	A549	lung
3	chr17:19471200-19482800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr17:19476600-19482800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr17:19481000-19483400	Enhancers	Liver	Liver
6	chr17:19481200-19485600	Weak transcription	HepG2	liver
7	chr17:19481800-19482800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr17:19482000-19482800	Enhancers	Colon Smooth Muscle	Colon
9	chr17:19482200-19483400	Bivalent Enhancer	Fetal Stomach	stomach
10	chr17:19482400-19482800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr17:19482400-19482800	Enhancers	Brain Anterior Caudate	brain
12	chr17:19482400-19482800	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
13	chr17:19482600-19482800	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr17:19482600-19482800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr17:19482600-19482800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr17:19482600-19482800	Enhancers	Gastric	stomach
17	chr17:19482600-19482800	Bivalent Enhancer	NHEK	skin
18	chr17:19482600-19483000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
19	chr17:19482600-19483000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr17:19482600-19483000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr17:19482600-19483000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr17:19482600-19483000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr17:19482600-19483000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr17:19482600-19483000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr17:19482600-19483000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr17:19482600-19483200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr17:19482600-19483200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
28	chr17:19482600-19483200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
29	chr17:19482600-19483200	Bivalent Enhancer	Fetal Brain Male	brain
30	chr17:19482600-19483400	Bivalent/Poised TSS	Colonic Mucosa	Colon
31	chr17:19482600-19483400	Enhancers	Lung	lung
32	chr17:19482600-19483800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
33	chr17:19482600-19483800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
34	chr17:19482600-19484000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
35	chr17:19482600-19484000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
36	chr17:19482600-19484000	Bivalent Enhancer	Placenta	Placenta

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