Variant report

Variant	rs4944662
Chromosome Location	chr11:86740573-86740574
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	chr11:86729696..86732227-chr11:86739805..86742002,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10466732	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10751146	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10792898	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10792899	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12790462	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1378879	0.88[CEU][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs1531146	0.82[CEU][hapmap]
rs1551503	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1963952	0.82[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2001411	0.88[CEU][hapmap]
rs2034848	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2445575	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2445586	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs2445589	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2512330	0.80[EUR][1000 genomes]
rs2512332	0.80[EUR][1000 genomes]
rs2512356	0.82[CEU][hapmap]
rs2512358	0.82[CEU][hapmap]
rs2512365	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2512367	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2512396	0.87[CEU][hapmap]
rs2512485	0.88[CEU][hapmap]
rs2513210	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs2513214	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2513215	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2513216	0.91[EUR][1000 genomes]
rs2513228	0.88[CEU][hapmap];0.84[MEX][hapmap]
rs2513240	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs3133361	0.88[EUR][1000 genomes]
rs4245428	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4245429	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4245430	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4943971	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs71460024	0.85[AMR][1000 genomes]
rs7927570	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7943307	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7943346	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7943831	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7949018	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs921873	0.85[AMR][1000 genomes]
rs991773	0.93[AMR][1000 genomes];0.91[EUR][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	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	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
4	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
rs4944662	TMEM126A	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86731800-86748200	Weak transcription	Fetal Muscle Leg	muscle
2	chr11:86735800-86748200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:86738800-86741400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:86739200-86740600	Enhancers	NHEK	skin
5	chr11:86739200-86742000	Enhancers	HMEC	breast
6	chr11:86739400-86741000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:86739600-86740600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr11:86739600-86740800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:86739800-86741000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr11:86739800-86741400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr11:86740000-86740600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:86740000-86740600	Enhancers	Brain Cingulate Gyrus	brain
13	chr11:86740000-86740600	Flanking Active TSS	HepG2	liver
14	chr11:86740200-86740600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:86740400-86740600	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links