Variant report

Variant	rs12518034
Chromosome Location	chr5:93916953-93916954
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10035632	0.87[ASN][1000 genomes]
rs10035650	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10037228	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10039801	1.00[CHB][hapmap]
rs10041262	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041551	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs10041843	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10043779	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs10044797	0.90[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10051931	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10053484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10056685	0.91[CEU][hapmap]
rs10058130	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10058618	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10061737	0.87[ASN][1000 genomes]
rs10062248	0.87[ASN][1000 genomes]
rs10070258	0.91[CEU][hapmap]
rs10076188	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs10076461	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078049	0.87[ASN][1000 genomes]
rs10078304	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs10476612	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10476613	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10476615	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11949227	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11955373	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs11960129	0.87[ASN][1000 genomes]
rs12516225	0.88[CEU][hapmap]
rs12517866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13169956	0.87[ASN][1000 genomes]
rs13353994	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13354061	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13358642	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361811	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13362556	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083818	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs28645132	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28787271	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs306573	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs306575	0.91[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.87[ASN][1000 genomes]
rs4869215	0.99[AFR][1000 genomes]
rs55974730	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6862592	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873364	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs755898	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7705424	0.91[CEU][hapmap]
rs7711380	0.84[LWK][hapmap]
rs7725095	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs7725698	0.81[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7737779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9314117	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]

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	nsv1023191	chr5:93351646-93947928	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv537808	chr5:93351646-93947928	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv2758002	chr5:93765205-94042201	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	esv2759354	chr5:93765205-94042201	Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv534495	chr5:93789736-93962131	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv598952	chr5:93823951-93956986	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	esv2534212	chr5:93916020-93917734	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12518034	ANKRD32	cis	multi-tissue	Pritchard
rs12518034	ARSK	cis	parietal	SCAN
rs12518034	C5orf36	cis	cerebellum	SCAN
rs12518034	MCTP1	Cis_1M	lymphoblastoid	RTeQTL
rs12518034	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL
rs12518034	FAM172A	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93903000-93919800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:93909800-93918800	Weak transcription	Pancreas	Pancrea
3	chr5:93914200-93918800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr5:93914600-93917800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:93914600-93920200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:93915400-93917800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr5:93915800-93917000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr5:93916600-93917000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr5:93916800-93917000	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr5:93916800-93917400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr5:93916800-93918000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:93916800-93918000	Enhancers	NHEK	skin

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