Variant report

Variant	rs13152154
Chromosome Location	chr4:77417756-77417757
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10031136	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11723732	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13146564	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1398017	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1849215	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1949137	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2136854	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4241593	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4859673	0.80[CEU][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4859674	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4859688	0.80[GIH][hapmap]
rs62300863	0.87[EUR][1000 genomes]
rs62300882	0.85[EUR][1000 genomes]
rs6532417	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6843293	0.95[CEU][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6847099	0.88[CHB][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759262	chr4:77264596-77455405	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv2757069	chr4:77392092-77455405	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13152154	FGF5	cis	cerebellum	SCAN
rs13152154	CCDC158	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77407000-77419600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:77407400-77421000	Weak transcription	HMEC	breast
3	chr4:77408000-77421200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:77413200-77419200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:77414000-77419000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:77414000-77419800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:77415200-77417800	Enhancers	Fetal Heart	heart
8	chr4:77416400-77419000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr4:77416400-77419200	Weak transcription	Fetal Lung	lung
10	chr4:77416400-77432800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:77416600-77422600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:77416800-77419800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:77417400-77418400	Enhancers	Stomach Mucosa	stomach
14	chr4:77417400-77421000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:77417600-77419200	Enhancers	Liver	Liver
16	chr4:77417600-77419800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:77417600-77421200	Weak transcription	Lung	lung

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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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