Variant report

Variant	rs661741
Chromosome Location	chr9:92782853-92782854
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10117261	0.82[GIH][hapmap]
rs10820817	0.86[AFR][1000 genomes]
rs10820826	0.96[YRI][hapmap]
rs10821475	0.82[GIH][hapmap]
rs10821501	0.84[AFR][1000 genomes]
rs10991697	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs1443364	0.84[AFR][1000 genomes]
rs17361084	0.82[AFR][1000 genomes]
rs4743823	0.92[YRI][hapmap]
rs4744020	0.83[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs496129	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs497510	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs552128	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs586750	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs652454	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs657899	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684476	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7021679	0.84[AFR][1000 genomes]
rs7030563	0.92[YRI][hapmap]
rs7866392	0.85[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap]
rs7874166	0.85[CEU][hapmap]
rs920753	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs661741	ROR2	cis	parietal	SCAN
rs661741	SYK	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92776800-92787200	Weak transcription	Esophagus	oesophagus
2	chr9:92780600-92784800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:92781000-92783800	Enhancers	Aorta	Aorta
4	chr9:92781200-92783000	Weak transcription	Primary B cells from cord blood	blood
5	chr9:92781200-92783400	Enhancers	HSMMtube	muscle
6	chr9:92781400-92783600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr9:92781400-92784000	Enhancers	HSMM	muscle
8	chr9:92781400-92784200	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr9:92781400-92784800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr9:92781400-92790400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:92781600-92783400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr9:92781600-92783800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr9:92781600-92784200	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr9:92781600-92786600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:92782000-92783600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr9:92782000-92783800	Enhancers	HMEC	breast
17	chr9:92782000-92784200	Enhancers	Left Ventricle	heart
18	chr9:92782200-92783400	Weak transcription	Psoas Muscle	Psoas
19	chr9:92782400-92783400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr9:92782600-92783600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr9:92782800-92783000	Weak transcription	NHEK	skin
22	chr9:92782800-92784800	Weak transcription	Primary monocytes fromperipheralblood	blood

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