Variant report

Variant	rs2332462
Chromosome Location	chr14:25459482-25459483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10143606	0.83[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs10147992	0.86[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs11159034	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs2004925	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]
rs2038700	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6574126	0.92[ASW][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7141943	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8017228	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs873102	0.86[CHD][hapmap];0.86[MKK][hapmap]
rs912304	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2332462	REM2	cis	cerebellum	SCAN
rs2332462	STXBP6	cis	parietal	SCAN
rs2332462	RNF31	cis	parietal	SCAN

Chromatin state (count:42 , 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	chr14:25451800-25470200	Weak transcription	HSMMtube	muscle
4	chr14:25452800-25470000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr14:25454800-25463000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr14:25455000-25462400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr14:25455000-25470200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr14:25455200-25461200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr14:25455800-25460200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr14:25455800-25461000	Weak transcription	Right Ventricle	heart
11	chr14:25455800-25462400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr14:25455800-25463000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr14:25455800-25464400	Weak transcription	Brain Substantia Nigra	brain
14	chr14:25456000-25460000	Weak transcription	Fetal Heart	heart
15	chr14:25456000-25461000	Weak transcription	Right Atrium	heart
16	chr14:25456000-25461800	Weak transcription	Gastric	stomach
17	chr14:25456000-25462200	Weak transcription	Brain Hippocampus Middle	brain
18	chr14:25456000-25462800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr14:25456000-25472800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr14:25456200-25460600	Weak transcription	Stomach Mucosa	stomach
21	chr14:25456400-25466200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr14:25456400-25472800	Weak transcription	Brain Angular Gyrus	brain
23	chr14:25456600-25461400	Weak transcription	Brain Anterior Caudate	brain
24	chr14:25456800-25459600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr14:25456800-25459800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr14:25457200-25459600	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr14:25457200-25460000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr14:25457200-25466200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr14:25457600-25459600	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr14:25457800-25459800	Strong transcription	Fetal Intestine Small	intestine
31	chr14:25458000-25461200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr14:25458000-25470200	Weak transcription	HepG2	liver
33	chr14:25458800-25459600	Strong transcription	Fetal Muscle Leg	muscle
34	chr14:25458800-25459600	Enhancers	Placenta	Placenta
35	chr14:25458800-25459600	Genic enhancers	Left Ventricle	heart
36	chr14:25459000-25459600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr14:25459000-25460200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr14:25459200-25460200	Enhancers	Pancreas	Pancrea
39	chr14:25459400-25462800	Weak transcription	HSMM	muscle
40	chr14:25459400-25466400	Weak transcription	Fetal Intestine Large	intestine
41	chr14:25459400-25468400	Weak transcription	Fetal Lung	lung
42	chr14:25459400-25470000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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