Variant report

Variant	rs2675399
Chromosome Location	chr2:189718962-189718963
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189715826..189717705-chr2:189717760..189720172,2	MCF-7	breast:
2	chr2:189717174..189718726-chr2:189718772..189720455,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10497682	0.82[AFR][1000 genomes]
rs11693891	0.85[AFR][1000 genomes]
rs11901190	0.86[AFR][1000 genomes]
rs12185550	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13012958	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1516439	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1516448	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1516449	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1516453	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16830657	0.82[AFR][1000 genomes]
rs16830658	0.81[AFR][1000 genomes]
rs17355585	0.82[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17760712	0.85[GIH][hapmap]
rs1850274	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2203600	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2351099	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2675395	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675400	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675401	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675404	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675405	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726558	0.81[AFR][1000 genomes]
rs6745069	0.81[AFR][1000 genomes]
rs7569201	1.00[ASN][1000 genomes]
rs7609094	0.81[AFR][1000 genomes]
rs781234	0.81[AFR][1000 genomes]
rs781280	0.89[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs781283	0.81[ASW][hapmap];0.89[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]

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	nsv1003974	chr2:189331760-189827814	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1008847	chr2:189603961-189769705	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv997454	chr2:189615728-189770133	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1002175	chr2:189615728-189776301	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv834490	chr2:189703550-189840963	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2675399	OR1N1	trans	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189714600-189719200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:189715800-189719000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:189716400-189719400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:189717000-189719200	Enhancers	NHDF-Ad	bronchial
5	chr2:189717400-189719200	Enhancers	NHLF	lung
6	chr2:189717600-189719000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:189717600-189719000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:189717600-189719200	Enhancers	Fetal Lung	lung

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