Variant report

Variant	rs4887052
Chromosome Location	chr15:78703631-78703632
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2009293	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4503760	1.00[CEU][hapmap]
rs4887049	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4887050	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55642616	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55832521	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62010380	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62010386	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62010387	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7179171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7183387	0.86[EUR][1000 genomes]
rs8042381	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv1627	chr15:78683761-78728604	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4887052	ETFA	cis	cerebellum	SCAN
rs4887052	SCAMP5	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78667600-78704400	Weak transcription	Lung	lung
2	chr15:78688000-78703800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:78692400-78705200	Weak transcription	Spleen	Spleen
4	chr15:78698200-78729800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:78700400-78706400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr15:78700800-78706400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:78700800-78722000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:78701600-78703800	Weak transcription	HMEC	breast
9	chr15:78701800-78703800	Weak transcription	NHEK	skin
10	chr15:78701800-78706400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr15:78702000-78706800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr15:78702800-78703800	Enhancers	Hela-S3	cervix
13	chr15:78702800-78704400	Enhancers	HUVEC	blood vessel
14	chr15:78703400-78705000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:78703600-78704400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:78703600-78704600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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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