Variant report

Variant	rs1963952
Chromosome Location	chr11:86726464-86726465
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:86724901..86726524-chr11:86747306..86749627,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166575	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10466732	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10751146	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10792898	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10792899	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12790462	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1378879	0.91[CHB][hapmap]
rs1551503	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001411	0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap]
rs2034848	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2445575	0.83[EUR][1000 genomes]
rs2445586	0.90[CHB][hapmap]
rs2445589	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2512356	0.91[CHB][hapmap]
rs2512358	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs2512365	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2512367	0.83[EUR][1000 genomes]
rs2512396	0.90[CHB][hapmap]
rs2512485	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2513210	0.91[CHB][hapmap];0.83[MEX][hapmap]
rs2513214	0.81[EUR][1000 genomes]
rs2513215	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2513216	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2513228	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs2513240	0.91[CHB][hapmap];0.83[MEX][hapmap]
rs3133361	0.80[EUR][1000 genomes]
rs4245428	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4245429	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4245430	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4463870	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4943971	0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs4944662	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71460024	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7927570	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7943307	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7943346	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7943831	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7949018	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs921873	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs991773	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2756074	chr11:86456552-86729552	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1037042	chr11:86586876-86978492	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv541119	chr11:86586876-86978492	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1963952	TMEM126A	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86711200-86727400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:86725000-86730400	Weak transcription	Right Atrium	heart
3	chr11:86725800-86730400	Weak transcription	Left Ventricle	heart
4	chr11:86725800-86730600	Weak transcription	Fetal Lung	lung
5	chr11:86726000-86730400	Weak transcription	Adipose Nuclei	Adipose
6	chr11:86726000-86730400	Weak transcription	Fetal Stomach	stomach
7	chr11:86726000-86730600	Weak transcription	Fetal Muscle Leg	muscle
8	chr11:86726000-86731000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:86726200-86728000	Weak transcription	HepG2	liver
10	chr11:86726200-86730600	Weak transcription	Fetal Heart	heart
11	chr11:86726200-86731400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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