Variant report

Variant	rs12167735
Chromosome Location	chr22:28616080-28616081
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10154425	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs10212007	0.86[EUR][1000 genomes]
rs10212036	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10212074	1.00[ASN][1000 genomes]
rs10212083	0.81[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10483143	1.00[ASW][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs12166023	1.00[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166077	0.89[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs12166158	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166253	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166719	0.89[CEU][hapmap];0.90[YRI][hapmap]
rs12166740	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs12166912	1.00[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168054	0.89[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168180	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12168652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168708	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12168851	0.93[AMR][1000 genomes]
rs12170022	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12170953	0.89[CEU][hapmap]
rs1297607	0.81[GIH][hapmap];1.00[MEX][hapmap]
rs134194	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs134197	1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs134488	0.81[GIH][hapmap];1.00[MEX][hapmap]
rs134506	0.81[GIH][hapmap];1.00[MEX][hapmap]
rs134514	0.86[GIH][hapmap];0.88[MEX][hapmap]
rs134547	0.93[GIH][hapmap];1.00[MEX][hapmap]
rs138642	0.83[AMR][1000 genomes]
rs16985967	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap]
rs16985976	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs16986037	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs16986077	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16986398	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs16987005	1.00[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17407024	0.88[CEU][hapmap];1.00[ASN][1000 genomes]
rs17483887	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs17484337	0.89[CEU][hapmap]
rs17487463	0.90[AMR][1000 genomes]
rs2143420	1.00[ASW][hapmap]
rs2345717	0.81[AMR][1000 genomes]
rs28579300	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55846737	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55856549	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56233401	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56391942	0.88[AMR][1000 genomes]
rs57686964	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58823697	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58936636	0.86[AFR][1000 genomes]
rs738200	0.81[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs73880387	0.81[EUR][1000 genomes]
rs73880391	1.00[ASN][1000 genomes]
rs73880393	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880395	1.00[ASN][1000 genomes]
rs73882704	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73882705	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73882709	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73882711	0.86[AFR][1000 genomes]
rs73882720	0.81[AFR][1000 genomes]
rs73882721	0.81[AFR][1000 genomes]
rs761322	1.00[ASN][1000 genomes]
rs761323	1.00[ASN][1000 genomes]
rs9306452	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs9620762	0.89[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs9620764	0.89[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs9620766	0.89[CEU][hapmap]
rs9620767	0.89[CEU][hapmap]
rs9620768	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs9620769	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620770	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[ASN][1000 genomes]
rs9620771	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620778	1.00[ASW][hapmap];0.81[CEU][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs9620779	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9625387	0.89[CEU][hapmap]
rs9625390	0.89[CEU][hapmap]
rs9625391	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs9625394	1.00[ASN][1000 genomes]
rs9625395	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9625403	0.89[CEU][hapmap]
rs9625405	1.00[ASN][1000 genomes]
rs9625406	1.00[ASN][1000 genomes]
rs9625407	1.00[ASN][1000 genomes]
rs9625408	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs9625409	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625410	1.00[ASN][1000 genomes]
rs9625413	1.00[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625415	0.81[EUR][1000 genomes]
rs9625416	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9625417	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9625418	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625421	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625425	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625427	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9625430	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9625433	1.00[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9625437	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9625440	0.90[AMR][1000 genomes]
rs9625441	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9625447	0.90[AMR][1000 genomes]
rs9625467	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs988893	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv459866	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv588879	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12167735	TTC28	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28600200-28616400	Weak transcription	Ovary	ovary
2	chr22:28604600-28617800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr22:28611800-28616400	Weak transcription	Left Ventricle	heart
4	chr22:28612200-28625600	Weak transcription	Aorta	Aorta
5	chr22:28612200-28634800	Weak transcription	Dnd41	blood
6	chr22:28612600-28616400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr22:28613800-28618800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr22:28614600-28618000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr22:28615000-28618000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr22:28615800-28626400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr22:28616000-28616600	Enhancers	Fetal Brain Female	brain

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