Variant report

Variant	rs17109462
Chromosome Location	chr14:25466465-25466466
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10132357	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10134048	0.83[TSI][hapmap]
rs10138510	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10151968	0.95[GIH][hapmap];0.87[TSI][hapmap]
rs11628502	0.94[ASN][1000 genomes]
rs11847576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11849185	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11850786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11850957	0.82[GIH][hapmap]
rs11851504	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17109371	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.94[ASN][1000 genomes]
rs17109380	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17109382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17109397	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17109401	0.81[CEU][hapmap]
rs17109406	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17109457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17109515	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs17109537	0.81[CEU][hapmap]
rs1952491	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1952499	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1958381	0.81[CEU][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap]
rs2077562	0.83[CEU][hapmap]
rs2093714	0.83[TSI][hapmap]
rs2094659	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28625718	0.94[ASN][1000 genomes]
rs28722832	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35106416	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57426267	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57614343	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58424382	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58590969	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7142073	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7152812	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7153837	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7154613	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7155485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7158164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs724116	0.83[TSI][hapmap]
rs8004566	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8008618	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8009099	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8019222	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8021478	0.83[TSI][hapmap]
rs987056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[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	nsv1041051	chr14:25388230-25480511	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1047792	chr14:25388933-25503799	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv901509	chr14:25398571-25743484	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17109462	PRMT5	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25451800-25470200	Weak transcription	HSMMtube	muscle
2	chr14:25452800-25470000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr14:25455000-25470200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr14:25456000-25472800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr14:25456400-25472800	Weak transcription	Brain Angular Gyrus	brain
6	chr14:25458000-25470200	Weak transcription	HepG2	liver
7	chr14:25459400-25468400	Weak transcription	Fetal Lung	lung
8	chr14:25459400-25470000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr14:25459600-25470000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr14:25459600-25470000	Weak transcription	Fetal Muscle Leg	muscle
11	chr14:25459800-25470000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr14:25461400-25467400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr14:25461400-25473200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr14:25461600-25472800	Weak transcription	Pancreas	Pancrea
15	chr14:25461600-25472800	Weak transcription	Right Atrium	heart
16	chr14:25463000-25470000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr14:25463200-25476600	Weak transcription	Placenta	Placenta
18	chr14:25463400-25469800	Weak transcription	Brain Anterior Caudate	brain
19	chr14:25464000-25470400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr14:25464600-25467400	Weak transcription	Brain Hippocampus Middle	brain
21	chr14:25464600-25469600	Weak transcription	Left Ventricle	heart
22	chr14:25464600-25472800	Weak transcription	Right Ventricle	heart
23	chr14:25465200-25467600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr14:25466200-25466600	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr14:25466200-25466600	Enhancers	Duodenum Mucosa	Duodenum
26	chr14:25466200-25466600	Enhancers	Psoas Muscle	Psoas
27	chr14:25466200-25466800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr14:25466400-25466600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr14:25466400-25466800	Enhancers	Brain Substantia Nigra	brain
30	chr14:25466400-25466800	Enhancers	Fetal Intestine Large	intestine
31	chr14:25466400-25466800	Enhancers	Fetal Intestine Small	intestine

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