Variant report

Variant	rs1559631
Chromosome Location	chr2:53416255-53416256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1364662	0.81[ASN][1000 genomes]
rs1364663	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs171877	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1834277	0.90[ASN][1000 genomes]
rs1863178	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1863179	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1863180	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs195572	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs195573	0.84[ASN][1000 genomes]
rs195574	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs195576	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs195577	0.88[ASN][1000 genomes]
rs2113420	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7562698	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7574564	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs933786	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs933788	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520722	chr2:53039770-53421015	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2751897	chr2:53358205-53475338	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1011032	chr2:53384170-53433055	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1002145	chr2:53387912-53832213	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv535718	chr2:53387912-53832213	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1559631	PRDXDD1P	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53413400-53416400	Enhancers	Fetal Kidney	kidney
2	chr2:53414600-53417000	Enhancers	Fetal Stomach	stomach
3	chr2:53414800-53417400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:53414800-53417600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:53415800-53416600	Enhancers	Fetal Lung	lung
6	chr2:53416000-53416400	Enhancers	Fetal Brain Male	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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