Variant report

Variant	rs2796525
Chromosome Location	chr1:57128620-57128621
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10157962	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12085402	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114167	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2206969	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2206970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2223779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404995	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2746337	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2746341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2746346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796497	0.91[EUR][1000 genomes]
rs2796502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796526	0.91[EUR][1000 genomes]
rs2796535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796536	1.00[EUR][1000 genomes]
rs2796543	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs857131	1.00[EUR][1000 genomes]
rs857133	0.91[EUR][1000 genomes]
rs857149	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs857154	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs857158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963527	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv523032	chr1:57116909-57249558	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2796525	PKP3	trans	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57120000-57132800	Weak transcription	Right Atrium	heart
2	chr1:57122400-57129200	Weak transcription	Psoas Muscle	Psoas
3	chr1:57122800-57169600	Weak transcription	Ovary	ovary
4	chr1:57123000-57131400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:57123000-57141800	Weak transcription	Hela-S3	cervix
6	chr1:57123000-57142000	Weak transcription	A549	lung
7	chr1:57123000-57143400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:57125600-57169800	Weak transcription	Aorta	Aorta
9	chr1:57126400-57130400	Weak transcription	Fetal Heart	heart
10	chr1:57126800-57128800	Weak transcription	Left Ventricle	heart
11	chr1:57128200-57129200	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr1:57128600-57129200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr1:57128600-57129200	Enhancers	HepG2	liver

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