Variant report

Variant	rs2004925
Chromosome Location	chr14:25445362-25445363
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10143606	0.86[JPT][hapmap]
rs10147992	0.82[JPT][hapmap]
rs11159034	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs2038700	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2332462	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6574126	0.92[ASW][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7141943	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8017228	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs873102	0.86[MKK][hapmap]
rs912304	0.86[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2004925	STXBP6	cis	parietal	SCAN
rs2004925	REM2	cis	cerebellum	SCAN
rs2004925	RNF31	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25424600-25460600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr14:25430000-25465800	Weak transcription	Lung	lung
3	chr14:25435800-25447400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr14:25436200-25447000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr14:25436200-25448000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr14:25436200-25451200	Weak transcription	A549	lung
7	chr14:25436600-25454200	Weak transcription	Fetal Muscle Leg	muscle
8	chr14:25436600-25454400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr14:25436600-25455400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr14:25436800-25451200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr14:25437200-25448000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr14:25438200-25448000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr14:25441000-25454200	Weak transcription	Fetal Brain Male	brain
14	chr14:25443000-25445400	Enhancers	Fetal Heart	heart
15	chr14:25443200-25445400	Enhancers	Colon Smooth Muscle	Colon
16	chr14:25443600-25445800	Weak transcription	Small Intestine	intestine
17	chr14:25443600-25446200	Weak transcription	HepG2	liver
18	chr14:25443800-25451400	Weak transcription	Left Ventricle	heart
19	chr14:25443800-25451400	Weak transcription	HSMM	muscle
20	chr14:25444000-25450400	Weak transcription	Pancreas	Pancrea
21	chr14:25444000-25451800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr14:25444200-25448800	Weak transcription	Fetal Lung	lung
23	chr14:25444200-25454600	Weak transcription	Right Atrium	heart
24	chr14:25444800-25449000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr14:25444800-25450400	Enhancers	Fetal Intestine Large	intestine
26	chr14:25445000-25445400	Enhancers	Brain Angular Gyrus	brain
27	chr14:25445000-25445400	Weak transcription	Brain Anterior Caudate	brain
28	chr14:25445000-25450600	Enhancers	Fetal Intestine Small	intestine
29	chr14:25445200-25445400	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr14:25445200-25454200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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