Variant report

Variant	rs706457
Chromosome Location	chr1:58920920-58920921
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs12126555	0.89[ASN][1000 genomes]
rs338248	0.82[EUR][1000 genomes]
rs6662936	0.82[EUR][1000 genomes]
rs6673660	0.81[EUR][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	nsv1008968	chr1:58582159-58982440	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv534974	chr1:58582159-58982440	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv829948	chr1:58803681-58971380	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv546314	chr1:58915624-58936384	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs706457	TACSTD2	cis	Thyroid	GTEx
rs706457	OMA1	cis	cerebellum	SCAN
rs706457	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL
rs706457	OMA1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58893400-58929200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr1:58898800-58929000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:58899000-58934200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr1:58906200-58932000	Weak transcription	Ovary	ovary
5	chr1:58914000-58930800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:58915400-58922600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:58918400-58974000	Weak transcription	Spleen	Spleen
8	chr1:58919000-58921200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:58919400-58921200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:58919400-58921200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:58919800-58923000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:58920000-58921000	Enhancers	H1 Cell Line	embryonic stem cell
13	chr1:58920000-58921000	Strong transcription	Lung	lung
14	chr1:58920400-58921200	Enhancers	Liver	Liver
15	chr1:58920400-58921200	Enhancers	Fetal Muscle Leg	muscle
16	chr1:58920400-58929000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:58920400-58934000	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:58920800-58922400	Strong transcription	Primary T cells from cord blood	blood

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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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