Variant report

Variant	rs1993539
Chromosome Location	chr3:55902452-55902453
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1350414	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1350415	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1458067	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1458068	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1870274	0.85[EUR][1000 genomes]
rs4955877	0.94[CHB][hapmap]
rs4955878	0.94[CHB][hapmap];0.89[TSI][hapmap]
rs57059589	0.85[EUR][1000 genomes]
rs72879133	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7432905	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9815001	0.82[CHB][hapmap]
rs9818424	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835091	0.85[CHB][hapmap]
rs9852746	0.82[CHB][hapmap]
rs9852888	0.82[CHB][hapmap]
rs9853067	0.86[CHB][hapmap]
rs9857973	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9881976	0.87[ASN][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	nsv1013063	chr3:55835413-56173713	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv876815	chr3:55895409-55979964	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1993539	IQCF1	cis	cerebellum	SCAN
rs1993539	HESX1	cis	cerebellum	SCAN
rs1993539	ERC2	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:55893000-55908800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:55893600-55923600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:55897600-55904600	Weak transcription	Brain Germinal Matrix	brain
4	chr3:55901200-55902600	Enhancers	Brain Hippocampus Middle	brain
5	chr3:55901400-55902800	Enhancers	Brain Cingulate Gyrus	brain
6	chr3:55901400-55903000	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr3:55902000-55902800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:55902200-55903400	Enhancers	Brain Anterior Caudate	brain
9	chr3:55902400-55902600	Enhancers	Brain Angular Gyrus	brain
10	chr3:55902400-55903200	Weak transcription	Brain Substantia Nigra	brain

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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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