Variant report

Variant	rs12896213
Chromosome Location	chr14:25388933-25388934
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11847172	0.81[GIH][hapmap]
rs17109307	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17109350	0.81[GIH][hapmap]
rs1951799	0.84[CEU][hapmap];0.82[GIH][hapmap]
rs1980712	0.95[CEU][hapmap];0.84[GIH][hapmap]
rs2057499	0.94[CEU][hapmap]
rs4983037	0.80[GIH][hapmap]
rs6650513	0.83[MEX][hapmap]
rs9285592	0.83[MEX][hapmap]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12896213	RNF31	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25379400-25397800	Weak transcription	Right Ventricle	heart
2	chr14:25381000-25389800	Weak transcription	Left Ventricle	heart
3	chr14:25381200-25389800	Weak transcription	Pancreas	Pancrea
4	chr14:25381400-25397800	Weak transcription	Fetal Intestine Small	intestine
5	chr14:25385800-25391000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr14:25386200-25389600	Enhancers	Fetal Heart	heart
7	chr14:25386200-25390200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr14:25386200-25391000	Weak transcription	HSMMtube	muscle
9	chr14:25386400-25389600	Weak transcription	HepG2	liver
10	chr14:25386400-25392600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr14:25386400-25393000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr14:25386600-25389800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr14:25387600-25391800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr14:25387800-25389000	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr14:25387800-25389400	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr14:25387800-25390600	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr14:25387800-25392000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr14:25388200-25389200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr14:25388200-25389800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr14:25388200-25393800	Weak transcription	Brain Substantia Nigra	brain
21	chr14:25388400-25389400	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr14:25388400-25389800	Weak transcription	Fetal Lung	lung
23	chr14:25388400-25389800	Weak transcription	Stomach Mucosa	stomach
24	chr14:25388400-25391000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr14:25388400-25392800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr14:25388400-25395000	Weak transcription	Brain Anterior Caudate	brain
27	chr14:25388600-25393800	Weak transcription	Brain Angular Gyrus	brain
28	chr14:25388600-25393800	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links