Variant report

Variant	rs657899
Chromosome Location	chr9:92786722-92786723
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10117261	0.82[GIH][hapmap]
rs10821475	0.82[GIH][hapmap]
rs4744020	0.81[MKK][hapmap]
rs496129	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs497510	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs552128	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs586750	0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601472	0.81[ASW][hapmap]
rs633926	0.81[ASW][hapmap]
rs652454	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs661741	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679273	0.81[ASW][hapmap]
rs684476	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7866392	0.85[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap]
rs7874166	0.85[CEU][hapmap]

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	nsv893561	chr9:92732368-92802101	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv482303	chr9:92752928-92890226	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv614852	chr9:92786722-93100550	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs657899	ROR2	cis	parietal	SCAN
rs657899	SYK	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92776800-92787200	Weak transcription	Esophagus	oesophagus
2	chr9:92781400-92790400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr9:92783000-92789000	Enhancers	Primary B cells from cord blood	blood
4	chr9:92783400-92787000	Enhancers	Primary B cells from peripheral blood	blood
5	chr9:92783400-92787800	Weak transcription	HSMMtube	muscle
6	chr9:92783600-92787200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr9:92784800-92786800	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr9:92784800-92788600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr9:92785000-92787200	Weak transcription	Gastric	stomach
10	chr9:92785400-92787600	Weak transcription	NHEK	skin
11	chr9:92786000-92787800	Enhancers	Duodenum Mucosa	Duodenum
12	chr9:92786000-92787800	Enhancers	GM12878-XiMat	blood
13	chr9:92786200-92787000	Weak transcription	Lung	lung
14	chr9:92786200-92788400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr9:92786400-92786800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr9:92786400-92786800	Weak transcription	Adipose Nuclei	Adipose
17	chr9:92786600-92787000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:92786600-92788200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links