Variant report

Variant	rs11159034
Chromosome Location	chr14:25488241-25488242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10142533	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10143606	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10147992	0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.89[MKK][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11159041	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1952490	0.83[ASN][1000 genomes]
rs1952492	0.81[CHD][hapmap];0.82[GIH][hapmap];0.82[ASN][1000 genomes]
rs2004925	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2038700	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2332462	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6574126	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs7141943	0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8017228	0.92[ASN][1000 genomes]
rs873102	0.83[CHB][hapmap];0.91[CHD][hapmap]
rs912304	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[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	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
5	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
6	nsv901510	chr14:25476170-25526309	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11159034	STXBP6	cis	parietal	SCAN
rs11159034	RNF31	cis	parietal	SCAN
rs11159034	EDDM3A	cis	cerebellum	SCAN
rs11159034	REM2	cis	cerebellum	SCAN
rs11159034	NOVA1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25479200-25488400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:25479400-25508600	Weak transcription	Brain Anterior Caudate	brain
3	chr14:25479600-25494800	Weak transcription	Stomach Mucosa	stomach
4	chr14:25479800-25501000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr14:25480000-25490000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr14:25480000-25490000	Weak transcription	Right Atrium	heart
7	chr14:25481200-25507400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr14:25484200-25488400	Weak transcription	Brain Hippocampus Middle	brain
9	chr14:25485200-25501600	Weak transcription	Fetal Intestine Small	intestine
10	chr14:25485400-25493600	Weak transcription	Fetal Lung	lung
11	chr14:25487200-25489200	Weak transcription	Pancreas	Pancrea
12	chr14:25487400-25489000	Weak transcription	Fetal Heart	heart
13	chr14:25487600-25489800	Weak transcription	Left Ventricle	heart
14	chr14:25488000-25489800	Weak transcription	Right Ventricle	heart
15	chr14:25488000-25505000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr14:25488200-25489800	Weak transcription	Aorta	Aorta
17	chr14:25488200-25490400	Enhancers	Fetal Brain Male	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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