Variant report

Variant	rs4347689
Chromosome Location	chr18:12216626-12216627
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 151 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs10445425	0.83[EUR][1000 genomes]
rs10445426	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]
rs11080549	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11080550	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11663077	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11876652	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs11877166	0.85[EUR][1000 genomes]
rs12454161	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12604417	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12605163	0.84[EUR][1000 genomes]
rs12605170	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12605187	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12605231	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12607481	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12955316	0.83[EUR][1000 genomes]
rs12963518	0.87[EUR][1000 genomes]
rs12965571	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs12969917	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs1986750	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs1986751	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs2006690	0.83[CEU][hapmap];0.89[CHB][hapmap]
rs2276369	0.85[EUR][1000 genomes]
rs2276370	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2849393	0.90[CHB][hapmap]
rs2849414	0.89[CHB][hapmap]
rs2849415	0.87[CEU][hapmap];0.84[CHB][hapmap]
rs2849416	0.82[CEU][hapmap];0.84[CHB][hapmap]
rs2849418	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs2849420	0.94[CHB][hapmap]
rs2851900	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs2851901	0.94[CHB][hapmap]
rs2851905	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2851907	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2851922	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs2851923	0.82[EUR][1000 genomes]
rs28592744	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28648884	0.84[EUR][1000 genomes]
rs3017858	0.84[EUR][1000 genomes]
rs34036584	0.84[EUR][1000 genomes]
rs34185303	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4239305	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4239307	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs4261610	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4296321	0.87[EUR][1000 genomes]
rs4299212	0.87[EUR][1000 genomes]
rs4303617	0.87[EUR][1000 genomes]
rs4306582	0.87[EUR][1000 genomes]
rs4327115	0.85[EUR][1000 genomes]
rs4337367	0.87[EUR][1000 genomes]
rs4402627	0.87[EUR][1000 genomes]
rs4416083	0.83[EUR][1000 genomes]
rs4417605	0.81[EUR][1000 genomes]
rs4417606	0.81[EUR][1000 genomes]
rs4419117	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[EUR][1000 genomes]
rs4456573	0.87[EUR][1000 genomes]
rs4462671	0.83[EUR][1000 genomes]
rs4464145	0.87[EUR][1000 genomes]
rs4480870	0.87[EUR][1000 genomes]
rs4519391	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4528645	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4528648	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes]
rs4538071	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs4569357	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4572475	0.87[EUR][1000 genomes]
rs4621045	0.83[EUR][1000 genomes]
rs4796945	0.81[EUR][1000 genomes]
rs4796946	0.82[EUR][1000 genomes]
rs4796947	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs4797615	0.89[CHB][hapmap]
rs4797624	0.84[EUR][1000 genomes]
rs4797625	0.83[EUR][1000 genomes]
rs4797631	0.87[EUR][1000 genomes]
rs4797632	0.87[EUR][1000 genomes]
rs4797633	0.87[EUR][1000 genomes]
rs4797634	0.87[EUR][1000 genomes]
rs4797636	0.87[EUR][1000 genomes]
rs4797637	0.87[EUR][1000 genomes]
rs4797640	0.81[EUR][1000 genomes]
rs55979571	0.82[EUR][1000 genomes]
rs56101236	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57801464	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60010024	0.82[EUR][1000 genomes]
rs60401418	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61606757	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62097608	0.85[EUR][1000 genomes]
rs62097613	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62099061	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62099085	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6505710	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs6505715	0.81[EUR][1000 genomes]
rs6505717	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6505720	0.85[EUR][1000 genomes]
rs6505725	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7226400	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7227857	0.86[EUR][1000 genomes]
rs7227955	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs7235017	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs7236715	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs7237912	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7239346	0.84[EUR][1000 genomes]
rs7239448	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7239947	0.87[EUR][1000 genomes]
rs7240093	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs7242225	0.96[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap]
rs7242541	0.82[EUR][1000 genomes]
rs7243248	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs7244723	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]
rs73410960	0.87[EUR][1000 genomes]
rs8082868	0.81[EUR][1000 genomes]
rs8082888	0.86[EUR][1000 genomes]
rs8083329	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs8083535	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs8083709	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8084532	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8087637	0.87[EUR][1000 genomes]
rs8091463	0.83[EUR][1000 genomes]
rs8091585	0.83[EUR][1000 genomes]
rs8093417	0.82[EUR][1000 genomes]
rs8095234	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs8095647	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[EUR][1000 genomes]
rs8098332	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8099792	0.84[EUR][1000 genomes]
rs9303759	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs9303760	0.82[EUR][1000 genomes]
rs949233	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs9945491	0.80[EUR][1000 genomes]
rs9948384	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs9949350	0.81[EUR][1000 genomes]
rs9951744	0.81[EUR][1000 genomes]
rs9951822	0.81[EUR][1000 genomes]
rs9951904	0.83[EUR][1000 genomes]
rs9951929	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs9954852	0.81[EUR][1000 genomes]
rs9954861	0.85[EUR][1000 genomes]
rs9954884	0.85[EUR][1000 genomes]
rs9955629	0.87[EUR][1000 genomes]
rs9956465	0.83[EUR][1000 genomes]
rs9956997	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]
rs9957303	0.83[EUR][1000 genomes]
rs9959641	0.83[EUR][1000 genomes]
rs9963587	0.82[EUR][1000 genomes]
rs9965004	0.82[EUR][1000 genomes]
rs9965108	0.84[EUR][1000 genomes]
rs9967372	0.87[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
rs4347689	RP11-64C12.3	cis	lung	GTEx

Chromatin state (count:3 , 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	chr18:12215000-12218600	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links