Variant report

Variant	rs2554465
Chromosome Location	chr8:52917469-52917470
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10104090	1.00[YRI][hapmap]
rs2280179	0.85[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2433235	0.81[ASN][1000 genomes]
rs2554462	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2677208	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2677209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs268924	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs268925	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs268926	0.80[ASN][1000 genomes]
rs6473675	0.80[JPT][hapmap];0.81[MEX][hapmap]
rs6473676	0.81[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.81[MEX][hapmap]
rs6473677	0.81[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.81[MEX][hapmap]
rs6982212	0.81[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.81[MEX][hapmap]
rs7005809	0.80[JPT][hapmap]
rs9298469	0.80[JPT][hapmap]

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	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1031672	chr8:52872448-52917469	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1020673	chr8:52878946-52917469	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1017700	chr8:52886765-52917469	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2554465	PXDNL	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52913200-52918600	Weak transcription	Fetal Thymus	thymus
2	chr8:52913400-52918800	Weak transcription	Thymus	Thymus
3	chr8:52913800-52920400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr8:52913800-52920600	Weak transcription	Primary T cells from cord blood	blood
5	chr8:52914600-52920000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr8:52914800-52920400	Weak transcription	GM12878-XiMat	blood
7	chr8:52916800-52920800	Weak transcription	Pancreas	Pancrea
8	chr8:52917400-52917800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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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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