Variant report

Variant	rs17277222
Chromosome Location	chr8:52567361-52567362
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10958289	0.99[ASN][1000 genomes]
rs10958290	0.99[ASN][1000 genomes]
rs13274571	0.87[ASN][1000 genomes]
rs16916856	1.00[ASW][hapmap]
rs17276712	0.91[ASN][1000 genomes]
rs4294172	0.99[ASN][1000 genomes]
rs4295654	0.99[ASN][1000 genomes]
rs4377955	0.93[ASN][1000 genomes]
rs4421345	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4517108	0.99[ASN][1000 genomes]
rs4636199	0.99[ASN][1000 genomes]
rs4873567	0.96[ASN][1000 genomes]
rs4873570	0.86[ASN][1000 genomes]
rs6473634	0.99[ASN][1000 genomes]
rs6981246	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6986081	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6987982	0.90[ASN][1000 genomes]
rs7005202	0.93[ASN][1000 genomes]
rs7010363	0.87[AMR][1000 genomes]
rs7010751	0.96[ASN][1000 genomes]
rs7012655	0.89[ASN][1000 genomes]
rs7014372	0.82[ASN][1000 genomes]
rs7018227	0.99[ASN][1000 genomes]
rs7834053	0.80[ASN][1000 genomes]
rs7838683	0.99[ASN][1000 genomes]
rs8180923	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932026	chr8:51858658-52758574	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv890895	chr8:52190571-52615191	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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
4	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers 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	19 gene(s)	inside rSNPs	diseases
5	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv831313	chr8:52458835-52638968	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17277222	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL
rs17277222	PXDNL	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52559600-52570400	Weak transcription	Left Ventricle	heart
2	chr8:52560400-52567800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr8:52562800-52568600	Enhancers	Fetal Heart	heart
4	chr8:52563400-52573400	Weak transcription	Right Atrium	heart
5	chr8:52564000-52567600	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr8:52565200-52567800	Weak transcription	Fetal Brain Male	brain
7	chr8:52566400-52580800	Weak transcription	Aorta	Aorta
8	chr8:52566800-52568200	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr8:52566800-52575200	Weak transcription	Fetal Lung	lung
10	chr8:52566800-52577400	Weak transcription	Psoas Muscle	Psoas

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