Variant report

Variant	rs2550670
Chromosome Location	chr12:56025191-56025192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10876839	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2550671	0.91[JPT][hapmap];0.91[YRI][hapmap]
rs2555037	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4759006	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]

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	nsv559001	chr12:55507465-56057708	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv948625	chr12:55838718-56118833	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2550670	LETMD1	cis	cerebellum	SCAN
rs2550670	NDUFA10	trans	cerebellum	SCAN
rs2550670	IKZF4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56017000-56026000	Weak transcription	Right Atrium	heart
2	chr12:56020600-56025200	Weak transcription	Right Ventricle	heart
3	chr12:56023000-56025400	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr12:56023200-56036800	Weak transcription	Spleen	Spleen
5	chr12:56023800-56025400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr12:56024400-56025400	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr12:56024800-56025800	Enhancers	Fetal Heart	heart
8	chr12:56025000-56026000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:56025000-56026600	Enhancers	Left 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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