Variant report

Variant	rs6871255
Chromosome Location	chr5:96736888-96736889
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10041189	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10044469	0.97[ASN][1000 genomes]
rs10055987	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10060043	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10063725	0.98[ASN][1000 genomes]
rs10073997	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10074671	0.98[ASN][1000 genomes]
rs10077749	0.99[ASN][1000 genomes]
rs11135510	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11135512	0.99[ASN][1000 genomes]
rs1113563	0.98[ASN][1000 genomes]
rs11744867	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11747458	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12332590	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12521282	0.90[ASN][1000 genomes]
rs13167465	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13186882	0.96[ASN][1000 genomes]
rs13357559	0.95[ASN][1000 genomes]
rs146689	0.84[ASN][1000 genomes]
rs17087524	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17087528	0.80[EUR][1000 genomes]
rs188344	0.99[ASN][1000 genomes]
rs2132225	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2220200	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28842623	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs291817	0.85[ASN][1000 genomes]
rs291819	0.84[ASN][1000 genomes]
rs4242236	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4362964	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4395658	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4607369	0.92[ASN][1000 genomes]
rs56050592	0.96[ASN][1000 genomes]
rs6556978	0.90[ASN][1000 genomes]
rs6859739	0.92[ASN][1000 genomes]
rs6865811	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6885295	0.99[ASN][1000 genomes]
rs6891107	0.92[ASN][1000 genomes]
rs6891837	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6893895	0.92[ASN][1000 genomes]
rs6895915	0.92[ASN][1000 genomes]
rs6898761	0.92[ASN][1000 genomes]
rs72779902	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72781909	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7718035	0.97[ASN][1000 genomes]
rs7721830	0.96[ASN][1000 genomes]
rs7721857	0.96[ASN][1000 genomes]
rs9314203	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1019790	chr5:96471680-96980633	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
3	nsv537812	chr5:96471680-96980633	ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv534326	chr5:96531217-97283481	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv882394	chr5:96538585-97108559	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1032548	chr5:96565121-97046804	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv537813	chr5:96565121-97046804	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv830415	chr5:96597763-96764157	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1025654	chr5:96613448-96817528	ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6871255	PCSK1	cis	parietal	SCAN
rs6871255	FAM172A	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96735200-96737000	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr5:96735200-96738400	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr5:96736000-96737800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:96736400-96737000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr5:96736600-96737000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:96736600-96737000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr5:96736600-96737000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr5:96736800-96737000	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr5:96736800-96737600	Enhancers	HUES64 Cell Line	embryonic stem cell

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