Variant report

Variant	rs4887041
Chromosome Location	chr15:78647962-78647963
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs28385476	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28428764	0.85[EUR][1000 genomes]
rs28534884	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2869028	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28709928	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4887042	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7176305	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
3	nsv833063	chr15:78605215-78754945	Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1052910	chr15:78608637-78707049	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4887041	SCAMP5	cis	cerebellum	SCAN
rs4887041	IMP3	cis	cerebellum	SCAN
rs4887041	CRABP1	cis	brain	BrainEAC
rs4887041	CRABP1	cis	thalamus	BrainEAC

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78634600-78652800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:78640800-78653200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:78641000-78650200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:78641000-78653400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:78641200-78650400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr15:78641200-78650400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:78641200-78650400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:78641200-78650400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr15:78641200-78650400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr15:78641200-78651400	Weak transcription	Fetal Kidney	kidney
11	chr15:78641400-78650400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:78641400-78650400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:78641400-78650400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:78641600-78650400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:78642400-78650400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr15:78645000-78658200	Weak transcription	Right Atrium	heart
17	chr15:78645800-78650600	Weak transcription	HepG2	liver
18	chr15:78646000-78650400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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

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