Variant report

Variant	rs12880456
Chromosome Location	chr14:25377188-25377189
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11847012	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1241598	0.93[CHB][hapmap]
rs12586425	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12588743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12880978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12883258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12885474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12886704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12887754	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12889054	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12891857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12893418	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12896576	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17185369	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17185376	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17185397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17257556	0.88[CEU][hapmap];0.93[CHB][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17257577	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951800	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4561376	0.84[GIH][hapmap]
rs58423583	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7141066	0.84[GIH][hapmap]
rs7154597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7155229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs74040723	0.97[ASN][1000 genomes]
rs8003472	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv901504	chr14:25184210-25646203	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv901506	chr14:25295551-25377188	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1041445	chr14:25326692-25388290	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv901508	chr14:25365505-25451903	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25362400-25378400	Weak transcription	Lung	lung
2	chr14:25364800-25379800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr14:25370200-25379800	Weak transcription	Brain Hippocampus Middle	brain
4	chr14:25370200-25379800	Weak transcription	Colon Smooth Muscle	Colon
5	chr14:25370200-25380400	Weak transcription	Right Atrium	heart
6	chr14:25370200-25380600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr14:25370400-25377200	Weak transcription	Adipose Nuclei	Adipose
8	chr14:25370400-25377600	Weak transcription	Fetal Lung	lung
9	chr14:25370400-25380600	Weak transcription	Brain Angular Gyrus	brain
10	chr14:25370800-25380200	Weak transcription	Brain Anterior Caudate	brain
11	chr14:25372600-25380600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr14:25372600-25382400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr14:25373400-25378600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr14:25373400-25380400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr14:25374000-25380400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr14:25374400-25378800	Weak transcription	Fetal Intestine Small	intestine
17	chr14:25374600-25377200	Weak transcription	HepG2	liver
18	chr14:25375200-25379000	Weak transcription	Fetal Heart	heart
19	chr14:25376200-25380400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr14:25376400-25377400	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr14:25376600-25377400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr14:25376800-25377200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr14:25377000-25378400	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr14:25377000-25378600	Enhancers	Left Ventricle	heart
25	chr14:25377000-25379800	Enhancers	Pancreas	Pancrea
26	chr14:25377000-25382000	Enhancers	Primary monocytes fromperipheralblood	blood

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