Variant report

Variant	rs854337
Chromosome Location	chr14:25330845-25330846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10459539	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs10483289	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs11158950	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1241584	0.86[EUR][1000 genomes]
rs1241585	0.84[EUR][1000 genomes]
rs1241586	0.86[EUR][1000 genomes]
rs1241587	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs1241589	0.86[EUR][1000 genomes]
rs1241590	0.86[EUR][1000 genomes]
rs1241591	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs1241592	0.86[EUR][1000 genomes]
rs1241593	0.87[EUR][1000 genomes]
rs1241595	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs1241596	0.96[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs1241597	0.96[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs1241599	0.96[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs1241600	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs1241601	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs1241602	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs1241603	0.87[EUR][1000 genomes]
rs1241604	0.96[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs1241606	0.95[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs1241607	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs1241609	0.87[EUR][1000 genomes]
rs1241610	0.84[CEU][hapmap]
rs1241611	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs1241612	0.83[CEU][hapmap]
rs1241614	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs1241646	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12879571	0.85[EUR][1000 genomes]
rs12879748	0.96[CEU][hapmap]
rs12879796	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs12880290	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs12880667	0.85[CHB][hapmap]
rs12884685	0.96[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs12888493	0.82[EUR][1000 genomes]
rs12888847	0.85[EUR][1000 genomes]
rs12888862	0.84[EUR][1000 genomes]
rs12888953	0.86[EUR][1000 genomes]
rs12889256	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs12889353	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs12894268	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs12894469	0.86[EUR][1000 genomes]
rs12895085	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs12895300	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs17257465	0.92[CHB][hapmap];0.89[ASN][1000 genomes]
rs8005503	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs8007588	0.86[MEX][hapmap]
rs8018496	0.93[MEX][hapmap]
rs854329	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.84[TSI][hapmap];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs854333	0.87[CEU][hapmap];0.93[MEX][hapmap];0.88[AMR][1000 genomes]
rs854334	0.89[ASW][hapmap];0.87[CEU][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs854338	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs854340	0.88[AFR][1000 genomes]
rs854342	0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs982467	0.92[CHB][hapmap];0.85[ASN][1000 genomes]
rs982468	0.92[CHB][hapmap];0.81[ASN][1000 genomes]
rs996271	0.86[EUR][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	nsv901505	chr14:25237268-25360584	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	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
6	nsv1041445	chr14:25326692-25388290	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs854337	PRMT5	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25314600-25333600	Weak transcription	Lung	lung
2	chr14:25317800-25344000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr14:25319600-25344600	Weak transcription	NHDF-Ad	bronchial
4	chr14:25321600-25333600	Weak transcription	Fetal Muscle Leg	muscle
5	chr14:25323600-25333600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr14:25326400-25343600	Weak transcription	Gastric	stomach
7	chr14:25328400-25331200	Enhancers	Right Ventricle	heart
8	chr14:25329200-25340000	Weak transcription	Brain Anterior Caudate	brain
9	chr14:25329200-25341800	Weak transcription	Right Atrium	heart
10	chr14:25329600-25331200	Enhancers	Placenta Amnion	Placenta Amnion
11	chr14:25329600-25331200	Enhancers	HSMM	muscle
12	chr14:25329800-25331000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr14:25329800-25331400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr14:25330000-25331000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr14:25330000-25331200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr14:25330000-25331200	Enhancers	NH-A	brain
17	chr14:25330200-25331000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr14:25330200-25331000	Enhancers	Duodenum Mucosa	Duodenum
19	chr14:25330200-25331000	Enhancers	Fetal Lung	lung
20	chr14:25330200-25331000	Enhancers	HepG2	liver
21	chr14:25330200-25331000	Enhancers	HSMMtube	muscle
22	chr14:25330200-25331200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr14:25330200-25331200	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr14:25330200-25331200	Enhancers	Fetal Intestine Large	intestine
25	chr14:25330200-25331200	Enhancers	Fetal Intestine Small	intestine
26	chr14:25330200-25331200	Flanking Active TSS	NHEK	skin
27	chr14:25330200-25331400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr14:25330400-25331000	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr14:25330400-25331000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr14:25330400-25331000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr14:25330400-25331000	Enhancers	Brain Angular Gyrus	brain
32	chr14:25330400-25331000	Enhancers	Brain Hippocampus Middle	brain
33	chr14:25330400-25331000	Enhancers	Colon Smooth Muscle	Colon
34	chr14:25330400-25331000	Enhancers	A549	lung
35	chr14:25330400-25331200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr14:25330400-25331200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr14:25330400-25331200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr14:25330400-25331200	Enhancers	Liver	Liver
39	chr14:25330400-25331200	Flanking Active TSS	Hela-S3	cervix
40	chr14:25330400-25332600	Enhancers	Stomach Mucosa	stomach
41	chr14:25330400-25334600	Enhancers	Fetal Thymus	thymus
42	chr14:25330600-25331400	Enhancers	Pancreas	Pancrea
43	chr14:25330800-25331000	Enhancers	Stomach Smooth Muscle	stomach
44	chr14:25330800-25331200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr14:25330800-25331200	Weak transcription	Left Ventricle	heart
46	chr14:25330800-25332800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr14:25330800-25332800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr14:25330800-25333200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr14:25330800-25344000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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