Variant report

Variant	rs28547162
Chromosome Location	chr15:78477310-78477311
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13329641	1.00[AMR][1000 genomes]
rs1973733	1.00[MEX][hapmap]
rs28377967	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28384144	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28408435	1.00[AMR][1000 genomes]
rs28544503	1.00[AMR][1000 genomes]
rs28588665	1.00[AMR][1000 genomes]
rs28625960	1.00[AMR][1000 genomes]
rs28674481	1.00[AMR][1000 genomes]
rs28676476	1.00[AMR][1000 genomes]
rs28696266	1.00[AMR][1000 genomes]
rs28706083	1.00[AMR][1000 genomes]
rs28781283	1.00[AMR][1000 genomes]
rs8040826	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv948437	chr15:78435527-78504662	Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv904430	chr15:78466127-78507316	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28547162	LOC100192378	trans	lymphoblastoid	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78470200-78486600	Weak transcription	Brain Hippocampus Middle	brain
2	chr15:78470400-78493800	Weak transcription	Brain Substantia Nigra	brain
3	chr15:78470600-78486600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr15:78475400-78483800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:78475400-78486200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:78475800-78483400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr15:78477000-78477600	Enhancers	Brain Cingulate Gyrus	brain
8	chr15:78477200-78477400	Enhancers	Brain Anterior Caudate	brain
9	chr15:78477200-78477400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

Quick Search:

Input of quick search could be:

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

what's new

Quick links