Variant report

Variant	rs13187808
Chromosome Location	chr5:117223828-117223829
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10057080	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12652888	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13170209	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13358274	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35415156	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4437413	0.81[CEU][hapmap];0.85[CHB][hapmap];0.87[GIH][hapmap]
rs6595069	0.94[EUR][1000 genomes]
rs6863742	0.83[GIH][hapmap]
rs7701120	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019332	chr5:116888074-117248632	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1027428	chr5:117072745-118036353	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv537877	chr5:117072745-118036353	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv882760	chr5:117087858-117292268	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1067621	chr5:117102544-118036352	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv531292	chr5:117102544-118036352	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv599490	chr5:117118798-117241490	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1027231	chr5:117144919-117375680	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv537878	chr5:117144919-117375680	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1033737	chr5:117148087-117274792	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv537879	chr5:117148087-117274792	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv882761	chr5:117152947-117241490	Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv1021370	chr5:117217907-117479218	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13187808	CCDC112	cis	parietal	SCAN
rs13187808	FTMT	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:117223400-117224000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr5:117223400-117224200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr5:117223600-117224000	Enhancers	Brain Anterior Caudate	brain
4	chr5:117223600-117224000	Enhancers	Fetal Lung	lung
5	chr5:117223600-117224000	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr5:117223600-117224200	Enhancers	Ovary	ovary
7	chr5:117223600-117224400	Enhancers	Brain Substantia Nigra	brain
8	chr5:117223600-117224600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr5:117223600-117225400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:117223800-117224000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr5:117223800-117224000	Enhancers	Rectal Smooth Muscle	rectum
12	chr5:117223800-117224000	Enhancers	NHLF	lung
13	chr5:117223800-117224200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:117223800-117224400	Enhancers	Primary hematopoietic stem cells	blood
15	chr5:117223800-117224600	Enhancers	Cortex derived primary cultured neurospheres	brain

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

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