Variant report

Variant	rs12185550
Chromosome Location	chr2:189716312-189716313
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:189712622..189715061-chr2:189715342..189717694,2	MCF-7	breast:
2	chr2:189471791..189474252-chr2:189714705..189717023,2	MCF-7	breast:
3	chr2:189715826..189717705-chr2:189717760..189720172,2	MCF-7	breast:
4	chr2:189468855..189473219-chr2:189714183..189718642,4	MCF-7	breast:
5	chr2:189714214..189716824-chr2:189837955..189840832,2	MCF-7	breast:
6	chr2:189466377..189468832-chr2:189715963..189717605,2	MCF-7	breast:
7	chr2:189468981..189471688-chr2:189714606..189717549,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168542	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10804024	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10931382	0.80[EUR][1000 genomes]
rs1157434	0.85[EUR][1000 genomes]
rs12619491	0.81[EUR][1000 genomes]
rs12998848	0.80[EUR][1000 genomes]
rs13001931	0.84[EUR][1000 genomes]
rs13012958	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13024524	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1516439	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1516448	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1516449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1516453	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1518006	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1518012	0.84[CEU][hapmap]
rs1524375	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1568235	0.80[EUR][1000 genomes]
rs1607316	0.83[AFR][1000 genomes]
rs17355585	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1850274	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177544	0.84[EUR][1000 genomes]
rs2203600	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2351099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675395	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2675399	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2675400	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2675401	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2675404	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2675405	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2708209	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3856335	0.81[EUR][1000 genomes]
rs4667249	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6757283	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7569201	1.00[ASN][1000 genomes]
rs981265	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	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

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189714000-189717600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr2:189714600-189719200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:189714800-189717600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:189715200-189716400	Enhancers	NHLF	lung
5	chr2:189715400-189716400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:189715600-189717400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:189715800-189717000	Weak transcription	NHDF-Ad	bronchial
8	chr2:189715800-189718600	Weak transcription	Fetal Stomach	stomach
9	chr2:189715800-189719000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:189716000-189716400	Enhancers	Fetal Lung	lung

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