Variant report

Variant	rs12885474
Chromosome Location	chr14:25381377-25381378
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:25379876..25382458-chr14:25394201..25396372,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11847012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];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];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12880456	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]
rs12880978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[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];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];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12887754	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12889054	0.88[AFR][1000 genomes];1.00[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];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12893418	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12896576	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17185369	0.89[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.84[AFR][1000 genomes];1.00[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];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17185397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17257556	0.93[ASW][hapmap];0.88[CEU][hapmap];0.93[CHB][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17257577	0.89[AFR][1000 genomes];1.00[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	0.88[AMR][1000 genomes];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];0.92[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];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1041445	chr14:25326692-25388290	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	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:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25372600-25382400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr14:25377000-25382000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr14:25377200-25381400	Enhancers	HepG2	liver
4	chr14:25378800-25381400	Enhancers	Fetal Intestine Small	intestine
5	chr14:25379000-25381400	Enhancers	Fetal Heart	heart
6	chr14:25379200-25381400	Enhancers	Fetal Intestine Large	intestine
7	chr14:25379400-25397800	Weak transcription	Right Ventricle	heart
8	chr14:25379800-25381400	Enhancers	Colon Smooth Muscle	Colon
9	chr14:25380000-25381400	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr14:25380000-25381400	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr14:25380200-25381400	Enhancers	Brain Substantia Nigra	brain
12	chr14:25380400-25381400	Enhancers	Liver	Liver
13	chr14:25380400-25381600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr14:25380400-25382600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr14:25380600-25381400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr14:25380600-25381400	Enhancers	Stomach Smooth Muscle	stomach
17	chr14:25380600-25381400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr14:25380600-25381600	Enhancers	Rectal Smooth Muscle	rectum
19	chr14:25380800-25381400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr14:25380800-25381400	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr14:25380800-25381400	Enhancers	Brain Germinal Matrix	brain
22	chr14:25380800-25381400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
23	chr14:25381000-25381400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr14:25381000-25381400	Enhancers	Duodenum Mucosa	Duodenum
25	chr14:25381000-25381400	Enhancers	NHEK	skin
26	chr14:25381000-25383000	Weak transcription	Psoas Muscle	Psoas
27	chr14:25381000-25383000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr14:25381000-25385400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr14:25381000-25389800	Weak transcription	Left Ventricle	heart
30	chr14:25381200-25381400	Active TSS	Brain Cingulate Gyrus	brain
31	chr14:25381200-25381400	Active TSS	Brain Hippocampus Middle	brain
32	chr14:25381200-25381400	Enhancers	HSMMtube	muscle
33	chr14:25381200-25381400	Enhancers	NHDF-Ad	bronchial
34	chr14:25381200-25381600	Enhancers	Muscle Satellite Cultured Cells	--
35	chr14:25381200-25381600	Enhancers	Colonic Mucosa	Colon
36	chr14:25381200-25382400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr14:25381200-25382600	Enhancers	Fetal Lung	lung
38	chr14:25381200-25383600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr14:25381200-25384000	Enhancers	HSMM	muscle
40	chr14:25381200-25384600	Enhancers	Brain Angular Gyrus	brain
41	chr14:25381200-25384800	Enhancers	Brain Anterior Caudate	brain
42	chr14:25381200-25385200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr14:25381200-25385200	Weak transcription	A549	lung
44	chr14:25381200-25385400	Weak transcription	Stomach Mucosa	stomach
45	chr14:25381200-25387800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr14:25381200-25388200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr14:25381200-25389800	Weak transcription	Pancreas	Pancrea

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