Variant report

Variant	rs909542
Chromosome Location	chr6:113756593-113756594
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:113753088..113757268-chr6:113951584..113954499,3	MCF-7	breast:
2	chr6:113750617..113753339-chr6:113755230..113758094,2	MCF-7	breast:
3	chr6:113755353..113757884-chr6:113758152..113760628,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230943	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1033390	0.87[CHD][hapmap]
rs1033391	0.87[CHD][hapmap]
rs10484458	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12175106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12214468	0.87[CHD][hapmap]
rs12526316	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12527509	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12528387	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1883170	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2049924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2142638	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2142640	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2179114	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2179115	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2179116	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2179117	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2294231	0.87[CHD][hapmap]
rs2348298	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348299	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348300	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348301	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4945951	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5001721	0.83[ASN][1000 genomes]
rs58748285	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6903255	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6925126	0.83[ASN][1000 genomes]
rs6928402	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724290	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs766330	0.83[ASN][1000 genomes]
rs7759869	0.87[CHD][hapmap]
rs7766686	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7776236	0.87[CHD][hapmap]
rs9320451	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9320452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320453	0.83[JPT][hapmap]
rs9320460	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9372363	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9372364	0.92[ASN][1000 genomes]
rs9374402	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9374403	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9374405	0.83[ASN][1000 genomes]
rs9384867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9384868	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9387146	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9387147	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9387149	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9398344	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9398345	0.82[ASN][1000 genomes]
rs9398346	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9398347	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9400626	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9400630	0.84[ASN][1000 genomes]
rs9488196	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9488198	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9488199	0.81[ASN][1000 genomes]
rs9488202	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916294	chr6:113518489-113904305	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1034256	chr6:113703567-113793790	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1021815	chr6:113703567-113799956	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1018357	chr6:113748468-113781070	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs909542	TEX101	trans	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:113753600-113756600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:113753600-113756800	Enhancers	Osteobl	bone
3	chr6:113753800-113756600	Enhancers	Fetal Lung	lung
4	chr6:113754200-113756800	Enhancers	Fetal Stomach	stomach
5	chr6:113755200-113756800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:113755400-113757000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:113755600-113756600	Weak transcription	Adipose Nuclei	Adipose
8	chr6:113755800-113757400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr6:113755800-113758800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:113755800-113767800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr6:113756000-113756800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:113756200-113762800	Weak transcription	A549	lung
13	chr6:113756400-113757200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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