Variant report

Variant	rs10147992
Chromosome Location	chr14:25503799-25503800
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10142533	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10143606	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11159034	0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.89[MKK][hapmap]
rs11159041	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1952492	0.81[ASW][hapmap];0.80[GIH][hapmap];0.80[TSI][hapmap]
rs2004925	0.82[JPT][hapmap]
rs2038700	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2332462	0.86[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs6574126	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs7141943	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs7147583	0.86[ASN][1000 genomes]
rs7158626	0.88[ASN][1000 genomes]
rs729368	0.91[ASN][1000 genomes]
rs8003236	0.86[ASN][1000 genomes]
rs8014755	0.86[ASN][1000 genomes]
rs873102	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs912304	0.87[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.89[MKK][hapmap];0.84[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

Variant related diseases (count:1)

Disease	PMID	Source
White blood cell types	21738478	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10147992	RNF31	cis	parietal	SCAN
rs10147992	STXBP6	cis	parietal	SCAN
rs10147992	EDDM3A	cis	cerebellum	SCAN
rs10147992	REM2	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25479400-25508600	Weak transcription	Brain Anterior Caudate	brain
2	chr14:25481200-25507400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr14:25488000-25505000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr14:25492400-25517600	Weak transcription	Psoas Muscle	Psoas
5	chr14:25495400-25507400	Weak transcription	Fetal Lung	lung
6	chr14:25497200-25515200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr14:25499800-25504600	Weak transcription	Right Ventricle	heart
8	chr14:25502000-25503800	Weak transcription	Left Ventricle	heart
9	chr14:25502000-25504400	Enhancers	HepG2	liver
10	chr14:25503400-25504000	Enhancers	Small Intestine	intestine
11	chr14:25503400-25505200	Enhancers	Fetal Intestine Large	intestine
12	chr14:25503400-25505600	Enhancers	Stomach Mucosa	stomach
13	chr14:25503600-25503800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr14:25503600-25504600	Enhancers	Pancreas	Pancrea
15	chr14:25503600-25505600	Enhancers	Fetal Intestine Small	intestine

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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