Variant report

Variant	rs2223779
Chromosome Location	chr1:57151856-57151857
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
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]
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]
rs2796525	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:4 , 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
3	esv1831276	chr1:57139370-57175158	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
4	nsv520726	chr1:57143986-57205666	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	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
rs2223779	PKP3	trans	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57122800-57169600	Weak transcription	Ovary	ovary
2	chr1:57125600-57169800	Weak transcription	Aorta	Aorta
3	chr1:57129800-57152200	Weak transcription	Psoas Muscle	Psoas
4	chr1:57135400-57160200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:57136200-57161400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:57143000-57153600	Weak transcription	NH-A	brain
7	chr1:57143600-57153600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:57144200-57165000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:57144200-57171800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:57144400-57169400	Weak transcription	Fetal Kidney	kidney
11	chr1:57144400-57173600	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:57148800-57152600	Enhancers	Hela-S3	cervix
13	chr1:57149600-57166000	Weak transcription	Right Ventricle	heart
14	chr1:57150000-57165800	Weak transcription	Left Ventricle	heart
15	chr1:57150600-57152000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:57150600-57152000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:57150600-57168000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:57151000-57165600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:57151400-57152200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:57151400-57153600	Enhancers	A549	lung
21	chr1:57151400-57165400	Weak transcription	Fetal Heart	heart
22	chr1:57151800-57152400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:57151800-57152400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr1:57151800-57152600	Enhancers	HepG2	liver
25	chr1:57151800-57152800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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