Variant report

Variant	rs1030090
Chromosome Location	chr2:56439314-56439315
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12713315	0.86[MEX][hapmap]
rs1549028	1.00[MEX][hapmap];0.86[MKK][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17047623	0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17047680	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2080606	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs214038	1.00[ASN][1000 genomes]
rs214045	1.00[ASN][1000 genomes]
rs214046	1.00[ASN][1000 genomes]
rs2216325	0.85[YRI][hapmap]
rs59813060	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545560	0.93[MEX][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759030	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs985792	1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[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	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv874162	chr2:56255832-56480571	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv874169	chr2:56383762-56473480	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1030090	FGF10	trans	cerebellum	SCAN
rs1030090	CCDC85A	cis	cerebellum	SCAN
rs1030090	CCDC85A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56420600-56443200	Weak transcription	Adipose Nuclei	Adipose
2	chr2:56423000-56443400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:56435600-56439600	Enhancers	Muscle Satellite Cultured Cells	--
4	chr2:56435800-56440000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:56437400-56439800	Enhancers	HUVEC	blood vessel
6	chr2:56438000-56439800	Weak transcription	Left Ventricle	heart
7	chr2:56438000-56443800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:56438400-56446200	Weak transcription	HSMM	muscle
9	chr2:56439200-56439800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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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

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