Variant report

Variant	rs658071
Chromosome Location	chr3:53509107-53509108
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12629138	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs2884712	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs312480	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs312485	0.95[ASN][1000 genomes]
rs4026181	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630080	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841726	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs658071	TKT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53508000-53511400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:53508000-53511600	Weak transcription	Fetal Intestine Small	intestine
3	chr3:53508000-53512200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:53508400-53511400	Weak transcription	HepG2	liver
5	chr3:53508800-53509600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr3:53508800-53509600	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr3:53508800-53509800	Enhancers	Brain Germinal Matrix	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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