Variant report

Variant	rs12433458
Chromosome Location	chr14:71323514-71323515
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10129495	0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs10131500	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10140775	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10141804	0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap]
rs10143748	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10147150	0.80[EUR][1000 genomes]
rs1018976	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10873243	0.85[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs11158882	0.85[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs11621281	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs11624934	0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs11625206	0.82[MEX][hapmap]
rs11628333	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12434514	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12879624	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12883778	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12886294	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12886990	0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs12895794	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12897648	0.83[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs17108492	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2158530	0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs2158531	0.85[CHB][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap]
rs35014968	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35386983	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36570	0.86[CHB][hapmap];0.95[CHD][hapmap]
rs4899377	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902843	0.82[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs4902846	0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs61194329	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71425222	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8019261	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs8019448	0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs8019513	0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs8020663	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs9323548	0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1049741	chr14:71233043-71462509	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1037839	chr14:71263886-71625114	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv542127	chr14:71263886-71625114	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1038007	chr14:71269747-71667680	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv1039769	chr14:71310954-71525720	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv542128	chr14:71310954-71525720	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv1053303	chr14:71316325-71402971	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12433458	PSEN1	cis	parietal	SCAN
rs12433458	DNAL1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71322600-71324600	Enhancers	HMEC	breast
2	chr14:71322800-71324600	Enhancers	HSMM	muscle
3	chr14:71322800-71324800	Enhancers	Muscle Satellite Cultured Cells	--
4	chr14:71323000-71324600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr14:71323000-71324600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr14:71323000-71324600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr14:71323000-71324600	Enhancers	HSMMtube	muscle
8	chr14:71323000-71324600	Enhancers	NH-A	brain
9	chr14:71323000-71324800	Enhancers	NHEK	skin
10	chr14:71323200-71324200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr14:71323200-71324400	Enhancers	NHDF-Ad	bronchial
12	chr14:71323200-71324600	Enhancers	Osteobl	bone
13	chr14:71323400-71324400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr14:71323400-71324400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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