Variant report

Variant	rs542036
Chromosome Location	chr15:43541139-43541140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 3 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs2176870	0.80[GIH][hapmap]

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	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs542036	MGA	cis	parietal	SCAN
rs542036	FRMD5	cis	parietal	SCAN
rs542036	WDR76	cis	parietal	SCAN
rs542036	ZNF690	cis	multi-tissue	Pritchard
rs542036	TGM5	cis	lymphoblastoid	seeQTL
rs542036	RPAP1	cis	parietal	SCAN
rs542036	CCNDBP1	cis	multi-tissue	Pritchard
rs542036	TGM7	cis	Esophagus Mucosa	GTEx
rs542036	C15orf52	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43532600-43541600	Weak transcription	K562	blood
2	chr15:43536800-43543400	Weak transcription	Esophagus	oesophagus
3	chr15:43538000-43546600	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr15:43540000-43541400	Enhancers	GM12878-XiMat	blood
5	chr15:43540400-43542600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:43540800-43542800	Enhancers	Primary hematopoietic stem cells	blood
7	chr15:43541000-43542600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:43541000-43542600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:43541000-43542800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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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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