Variant report

Variant	rs356669
Chromosome Location	chr9:98047793-98047794
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	chr9:98046120..98048579-chr9:98057469..98059283,2	K562	blood:
2	chr9:98046215..98048515-chr9:98048593..98050415,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10821450	0.81[AMR][1000 genomes]
rs1125753	0.90[GIH][hapmap]
rs171417	0.81[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes]
rs184818	0.81[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs187172	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2404692	0.91[GIH][hapmap]
rs356666	0.81[CHD][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs356673	0.81[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes]
rs356675	0.85[JPT][hapmap];0.91[AMR][1000 genomes]
rs356677	0.81[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes]
rs356678	0.81[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes]
rs356679	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs356680	0.81[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes]
rs356682	0.89[AMR][1000 genomes]
rs356683	0.91[AMR][1000 genomes]
rs356684	0.85[JPT][hapmap];0.91[AMR][1000 genomes]
rs356687	0.87[AMR][1000 genomes]
rs356688	0.91[AMR][1000 genomes]
rs356689	0.81[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs416792	0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs437511	0.91[AMR][1000 genomes]
rs4647376	0.81[JPT][hapmap];0.82[TSI][hapmap]
rs526189	0.87[AMR][1000 genomes]
rs540412	1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes]
rs565293	0.81[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes]
rs609324	0.89[AMR][1000 genomes]
rs657637	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs944934	1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs356669	SYK	cis	parietal	SCAN
rs356669	C9orf130	cis	parietal	SCAN
rs356669	TDRD7	cis	cerebellum	SCAN
rs356669	PHF2	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98045400-98048800	Enhancers	Fetal Intestine Large	intestine
2	chr9:98045800-98048800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:98046000-98048000	Enhancers	Fetal Intestine Small	intestine
4	chr9:98046200-98050200	Enhancers	Liver	Liver
5	chr9:98046600-98048200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:98046600-98048800	Weak transcription	Small Intestine	intestine
7	chr9:98046600-98059400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:98046600-98063000	Weak transcription	Fetal Stomach	stomach
9	chr9:98046800-98048200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:98047000-98048200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:98047000-98048200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:98047000-98048800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:98047200-98048200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr9:98047200-98048200	Weak transcription	A549	lung
15	chr9:98047200-98048200	Enhancers	NHLF	lung
16	chr9:98047200-98059400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:98047400-98047800	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:98047400-98047800	Enhancers	Duodenum Mucosa	Duodenum
19	chr9:98047400-98048000	Weak transcription	Fetal Lung	lung
20	chr9:98047400-98055800	Weak transcription	HepG2	liver
21	chr9:98047600-98048000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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