Variant report

Variant	rs261998
Chromosome Location	chr5:95898769-95898770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs155216	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs155217	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs155218	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570461	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2570463	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs261223	0.99[EUR][1000 genomes]
rs261226	0.89[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs261227	0.89[EUR][1000 genomes]
rs261238	0.86[EUR][1000 genomes]
rs261246	0.87[EUR][1000 genomes]
rs261995	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs261996	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs261997	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs261999	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs262000	0.99[EUR][1000 genomes]
rs263375	0.80[EUR][1000 genomes]
rs263377	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs263382	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs263383	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs263388	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs263389	0.86[ASN][1000 genomes]
rs263391	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs263394	0.83[ASN][1000 genomes]
rs263397	0.90[ASN][1000 genomes]
rs2882360	0.87[EUR][1000 genomes];0.97[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	nsv1030444	chr5:95353620-95995619	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv537810	chr5:95353620-95995619	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv1026484	chr5:95759910-95961518	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs261998	PCSK1	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95897800-95899200	Enhancers	NH-A	brain
2	chr5:95897800-95900600	Enhancers	Osteobl	bone
3	chr5:95897800-95902600	Enhancers	HUVEC	blood vessel
4	chr5:95898000-95898800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:95898000-95898800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:95898000-95898800	Enhancers	Hela-S3	cervix
7	chr5:95898000-95898800	Enhancers	NHLF	lung
8	chr5:95898000-95899600	Enhancers	NHDF-Ad	bronchial
9	chr5:95898000-95900000	Enhancers	HSMM	muscle
10	chr5:95898200-95898800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:95898200-95898800	Enhancers	Placenta Amnion	Placenta Amnion
12	chr5:95898200-95898800	Enhancers	A549	lung
13	chr5:95898200-95900000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:95898200-95903200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:95898400-95898800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:95898400-95901400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:95898600-95898800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:95898600-95898800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr5:95898600-95899200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:95898600-95901800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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