Variant report

Variant	rs1890074
Chromosome Location	chr9:16619009-16619010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1029015	0.88[CEU][hapmap];0.89[CHB][hapmap];0.82[EUR][1000 genomes]
rs10756772	0.87[EUR][1000 genomes]
rs10756773	0.84[CEU][hapmap];0.95[CHB][hapmap];0.85[EUR][1000 genomes]
rs10810579	0.95[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs10962519	0.83[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap]
rs10962520	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs11790341	0.95[CHB][hapmap]
rs13290470	0.95[CHB][hapmap];0.80[CHD][hapmap];0.86[ASN][1000 genomes]
rs1415471	0.88[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2050617	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs2275256	0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs4961727	0.84[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4961728	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs7019299	0.95[CHB][hapmap]
rs7033512	0.95[CHB][hapmap];0.84[CHD][hapmap]
rs7043298	0.84[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs9886876	0.88[CEU][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv430000	chr9:16603483-16671045	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1890074	SEC23A	trans	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16609600-16619800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr9:16611400-16626400	Weak transcription	Aorta	Aorta
3	chr9:16611800-16619600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr9:16613000-16619600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr9:16613000-16624800	Weak transcription	NH-A	brain
6	chr9:16613200-16624800	Weak transcription	A549	lung
7	chr9:16613800-16625600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr9:16614000-16619200	Weak transcription	HSMMtube	muscle
9	chr9:16614000-16624200	Weak transcription	HSMM	muscle
10	chr9:16614000-16624600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:16614200-16619200	Weak transcription	NHLF	lung
12	chr9:16614400-16625400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:16614600-16619200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr9:16615400-16619800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr9:16615600-16625400	Weak transcription	Psoas Muscle	Psoas
16	chr9:16618000-16619200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:16618000-16621400	Enhancers	Fetal Stomach	stomach
18	chr9:16618400-16620000	Enhancers	Muscle Satellite Cultured Cells	--
19	chr9:16618400-16620400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:16618400-16620600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:16618400-16620600	Enhancers	Fetal Kidney	kidney
22	chr9:16618400-16621200	Enhancers	Colon Smooth Muscle	Colon
23	chr9:16618600-16619200	Enhancers	Fetal Intestine Large	intestine
24	chr9:16618600-16620600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:16618600-16620800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:16618600-16621200	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr9:16618600-16625400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr9:16618800-16619200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:16618800-16619800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr9:16618800-16619800	Weak transcription	Ovary	ovary
31	chr9:16618800-16620000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr9:16618800-16620200	Enhancers	HUVEC	blood vessel
33	chr9:16618800-16620600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:16618800-16620600	Enhancers	Fetal Lung	lung
35	chr9:16618800-16621200	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr9:16618800-16621200	Enhancers	Rectal Smooth Muscle	rectum
37	chr9:16618800-16621800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr9:16618800-16623200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr9:16618800-16625400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr9:16619000-16620400	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr9:16619000-16620400	Enhancers	Osteobl	bone
42	chr9:16619000-16620600	Enhancers	Stomach Smooth Muscle	stomach

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