Variant report

Variant	rs12311080
Chromosome Location	chr12:43174747-43174748
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:43173451..43175672-chr12:43183405..43185439,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10506219	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11181672	0.91[EUR][1000 genomes]
rs11181673	0.83[EUR][1000 genomes]
rs11181674	0.91[EUR][1000 genomes]
rs11181675	0.89[EUR][1000 genomes]
rs11181676	0.91[EUR][1000 genomes]
rs11181677	0.91[EUR][1000 genomes]
rs11181678	0.83[ASW][hapmap];0.87[TSI][hapmap]
rs11181680	0.83[ASW][hapmap];0.88[TSI][hapmap]
rs11833302	0.84[EUR][1000 genomes]
rs12313884	0.91[EUR][1000 genomes]
rs12319782	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1356421	0.85[EUR][1000 genomes]
rs1356422	0.90[EUR][1000 genomes]
rs1356423	0.84[EUR][1000 genomes]
rs1607251	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1914486	0.83[EUR][1000 genomes]
rs1914487	0.85[EUR][1000 genomes]
rs2203734	0.85[EUR][1000 genomes]
rs2468330	0.95[ASN][1000 genomes]
rs2897590	0.82[ASW][hapmap];0.86[CEU][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs57284063	0.91[EUR][1000 genomes]
rs60367750	0.83[EUR][1000 genomes]
rs61924560	0.89[EUR][1000 genomes]
rs61926694	0.86[EUR][1000 genomes]
rs7137412	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953873	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7954424	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7963631	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7977054	0.84[EUR][1000 genomes]
rs868765	0.91[EUR][1000 genomes]
rs955918	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12311080	NELL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:43170000-43180200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr12:43172600-43174800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:43172600-43175400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:43172800-43175000	Enhancers	Fetal Heart	heart
5	chr12:43173000-43175000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:43173000-43175000	Enhancers	Ovary	ovary
7	chr12:43173200-43175000	Enhancers	Fetal Lung	lung
8	chr12:43173600-43174800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:43174200-43175600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:43174200-43179400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:43174200-43180600	Weak transcription	HSMM	muscle

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