Variant report

Variant	rs1980712
Chromosome Location	chr14:25406918-25406919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10483290	0.85[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs11847172	0.85[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12896213	0.95[CEU][hapmap];0.84[GIH][hapmap]
rs17109307	0.95[CEU][hapmap];0.87[GIH][hapmap]
rs17109350	0.85[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1951799	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2057499	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28491961	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28594628	0.85[ASN][1000 genomes]
rs28730543	0.82[ASN][1000 genomes]
rs28892979	0.84[ASN][1000 genomes]
rs4983037	0.85[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	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
6	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
7	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
rs1980712	RNF31	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25394800-25410400	Weak transcription	Fetal Muscle Leg	muscle
2	chr14:25395400-25410400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr14:25396600-25409200	Weak transcription	Left Ventricle	heart
4	chr14:25396600-25415800	Weak transcription	Fetal Brain Male	brain
5	chr14:25398000-25407800	Weak transcription	HSMMtube	muscle
6	chr14:25398200-25409400	Weak transcription	Fetal Lung	lung
7	chr14:25398400-25408600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr14:25399000-25410600	Weak transcription	Fetal Intestine Small	intestine
9	chr14:25399400-25413800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr14:25399800-25413400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr14:25399800-25413600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr14:25403800-25411400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr14:25403800-25411800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr14:25404600-25411800	Weak transcription	Brain Angular Gyrus	brain
15	chr14:25405200-25407200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr14:25405200-25408400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr14:25405200-25411800	Weak transcription	Brain Hippocampus Middle	brain
18	chr14:25405200-25411800	Weak transcription	Colon Smooth Muscle	Colon
19	chr14:25405400-25411800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr14:25405600-25408400	Weak transcription	Fetal Heart	heart
21	chr14:25405600-25409200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr14:25405600-25409200	Weak transcription	Right Ventricle	heart
23	chr14:25405600-25409800	Weak transcription	Pancreas	Pancrea
24	chr14:25405600-25410800	Weak transcription	HepG2	liver
25	chr14:25405600-25412400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr14:25406400-25412200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr14:25406800-25407200	Weak transcription	Brain Anterior Caudate	brain

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