Variant report

Variant	rs12140845
Chromosome Location	chr1:170112571-170112572
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	chr1:170111312..170113839-chr1:170118404..170121230,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263390	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12116611	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12116788	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12117652	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs12117699	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12120025	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12120968	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12121055	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12122794	0.83[EUR][1000 genomes]
rs12126443	0.88[CEU][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes]
rs12126954	0.95[EUR][1000 genomes]
rs12128116	0.83[EUR][1000 genomes]
rs12129144	0.83[EUR][1000 genomes]
rs12130116	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12131638	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs12132179	0.95[EUR][1000 genomes]
rs12132530	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12132575	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12133411	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12135203	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12135815	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12141501	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12141522	0.81[AMR][1000 genomes]
rs12141965	0.95[EUR][1000 genomes]
rs12142155	0.83[EUR][1000 genomes]
rs12144057	0.88[CEU][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes]
rs12144085	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs12145948	0.88[CEU][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes]
rs1411465	0.83[EUR][1000 genomes]
rs2150114	0.95[EUR][1000 genomes]
rs2421112	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41272485	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs488488	0.80[EUR][1000 genomes]
rs534412	0.95[EUR][1000 genomes]
rs56147946	0.85[EUR][1000 genomes]
rs688565	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv999310	chr1:170065943-170223350	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12140845	C1orf156	cis	lymphoblastoid	seeQTL
rs12140845	MGC9084	cis	multi-tissue	Pritchard
rs12140845	C1orf156	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170108800-170114000	Weak transcription	Fetal Heart	heart

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