Variant report

Variant	rs8028666
Chromosome Location	chr15:92890028-92890029
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10520710	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17702960	1.00[MKK][hapmap]
rs28396192	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28477680	0.92[ASN][1000 genomes]
rs7170557	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7170765	0.92[ASN][1000 genomes]
rs7182414	0.87[ASN][1000 genomes]
rs8030012	0.93[ASN][1000 genomes]
rs899527	0.87[ASN][1000 genomes]
rs899528	0.82[ASN][1000 genomes]
rs899529	0.86[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	nsv948621	chr15:92688981-93158095	Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1049561	chr15:92758434-93097965	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv1041582	chr15:92879844-92910306	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv869844	chr15:92881526-92935448	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8028666	ST8SIA2	cis	cerebellum	SCAN
rs8028666	C15orf58	cis	parietal	SCAN
rs8028666	IDH2	cis	cerebellum	SCAN
rs8028666	BLM	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92885800-92891800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:92887000-92890600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:92888200-92899400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:92888400-92890200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:92888600-92893600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:92888800-92890200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:92889600-92892200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr15:92889800-92891000	Enhancers	Fetal Heart	heart
9	chr15:92890000-92890400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr15:92890000-92890400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:92890000-92891400	Enhancers	Right Ventricle	heart

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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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