Variant report

Variant	rs12454161
Chromosome Location	chr18:12214808-12214809
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr18:12214700-12214976	GM12878	blood:	n/a	n/a
2	FOS	chr18:12214575-12214919	MCF10A-Er-Src	breast:	n/a	chr18:12214723-12214732
3	RUNX3	chr18:12214658-12214968	GM12878	blood:	n/a	chr18:12214784-12214799
4	STAT3	chr18:12214573-12214932	MCF10A-Er-Src	breast:	n/a	chr18:12214709-12214720
5	STAT3	chr18:12214625-12214929	MCF10A-Er-Src	breast:	n/a	chr18:12214709-12214720
6	FOS	chr18:12214574-12214912	MCF10A-Er-Src	breast:	n/a	chr18:12214723-12214732
7	STAT3	chr18:12214592-12214913	MCF10A-Er-Src	breast:	n/a	chr18:12214709-12214720

Variant related genes	Relation type
ENSG00000267733	TF binding region

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10445426	0.82[EUR][1000 genomes]
rs11080549	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11080550	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11877166	0.82[EUR][1000 genomes]
rs12604417	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12605163	0.83[EUR][1000 genomes]
rs12605170	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12605187	0.86[EUR][1000 genomes]
rs12605231	0.83[EUR][1000 genomes]
rs12607481	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12963518	0.83[EUR][1000 genomes]
rs2276369	0.87[EUR][1000 genomes]
rs2276370	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2851905	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2851907	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs28592744	0.83[EUR][1000 genomes]
rs28648884	0.81[EUR][1000 genomes]
rs3017858	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34036584	0.81[EUR][1000 genomes]
rs34185303	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4239305	0.81[EUR][1000 genomes]
rs4261610	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4296321	0.84[EUR][1000 genomes]
rs4299212	0.84[EUR][1000 genomes]
rs4303617	0.84[EUR][1000 genomes]
rs4306582	0.84[EUR][1000 genomes]
rs4327115	0.85[EUR][1000 genomes]
rs4337367	0.84[EUR][1000 genomes]
rs4347689	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4402627	0.84[EUR][1000 genomes]
rs4456573	0.84[EUR][1000 genomes]
rs4462671	0.85[EUR][1000 genomes]
rs4464145	0.84[EUR][1000 genomes]
rs4480870	0.84[EUR][1000 genomes]
rs4528645	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4538071	0.81[EUR][1000 genomes]
rs4569357	0.89[EUR][1000 genomes]
rs4572475	0.84[EUR][1000 genomes]
rs4797624	0.81[EUR][1000 genomes]
rs4797631	0.84[EUR][1000 genomes]
rs4797632	0.83[EUR][1000 genomes]
rs4797633	0.84[EUR][1000 genomes]
rs4797634	0.84[EUR][1000 genomes]
rs4797636	0.84[EUR][1000 genomes]
rs4797637	0.84[EUR][1000 genomes]
rs56101236	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57801464	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs60010024	0.82[EUR][1000 genomes]
rs60401418	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs61606757	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62097608	0.84[EUR][1000 genomes]
rs62097613	0.84[EUR][1000 genomes]
rs62099061	0.86[EUR][1000 genomes]
rs62099085	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6505720	0.81[EUR][1000 genomes]
rs6505725	0.86[EUR][1000 genomes]
rs7226400	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7227857	0.83[EUR][1000 genomes]
rs7237912	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7239346	0.81[EUR][1000 genomes]
rs7239448	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7239947	0.83[EUR][1000 genomes]
rs7240093	0.81[EUR][1000 genomes]
rs7243248	0.81[EUR][1000 genomes]
rs73410960	0.84[EUR][1000 genomes]
rs8082868	0.80[EUR][1000 genomes]
rs8082888	0.83[EUR][1000 genomes]
rs8083709	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs8084532	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs8087637	0.84[EUR][1000 genomes]
rs8098332	0.86[AFR][1000 genomes]
rs8099792	0.83[EUR][1000 genomes]
rs9303759	0.81[EUR][1000 genomes]
rs9954861	0.81[EUR][1000 genomes]
rs9954884	0.81[EUR][1000 genomes]
rs9955629	0.83[EUR][1000 genomes]
rs9965108	0.81[EUR][1000 genomes]
rs9967372	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv1055343	chr18:12107012-12226356	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
4	nsv960252	chr18:12161216-12220798	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	nsv909401	chr18:12211483-12312075	Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv909402	chr18:12211483-12325222	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12454161	RP11-64C12.3	cis	lung	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12209200-12217400	Weak transcription	NHEK	skin
2	chr18:12209400-12218600	Weak transcription	Hela-S3	cervix
3	chr18:12213200-12216000	Weak transcription	Fetal Heart	heart
4	chr18:12214400-12215000	Enhancers	HMEC	breast
5	chr18:12214400-12215200	Enhancers	GM12878-XiMat	blood
6	chr18:12214800-12215000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived

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