Variant report

Variant	rs4873584
Chromosome Location	chr8:52639744-52639745
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:52638232..52640953-chr8:52662899..52665475,2	MCF-7	breast:
2	chr8:52639137..52641125-chr8:52641198..52643184,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10090123	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10090972	0.82[EUR][1000 genomes]
rs10091454	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10106091	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10109862	0.88[EUR][1000 genomes]
rs10958295	0.85[EUR][1000 genomes]
rs10958296	0.92[EUR][1000 genomes]
rs10958297	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1317774	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13251960	0.81[EUR][1000 genomes]
rs13270001	0.92[EUR][1000 genomes]
rs13277004	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13279413	0.81[EUR][1000 genomes]
rs16916741	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16916763	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28512421	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28549751	0.81[EUR][1000 genomes]
rs28616568	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2976209	0.94[EUR][1000 genomes]
rs34342438	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34998867	0.81[EUR][1000 genomes]
rs35195931	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36075262	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4242472	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4326377	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4397396	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4400372	0.92[EUR][1000 genomes]
rs4873201	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4873572	0.91[EUR][1000 genomes]
rs4873575	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55701628	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6981260	0.92[EUR][1000 genomes]
rs6986571	0.92[EUR][1000 genomes]
rs6986605	0.92[EUR][1000 genomes]
rs6999693	0.92[EUR][1000 genomes]
rs7005788	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7007671	0.92[EUR][1000 genomes]
rs7007804	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7011666	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7839661	0.82[EUR][1000 genomes]
rs9643788	0.87[AMR][1000 genomes];0.94[EUR][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	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	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
3	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
4	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
5	nsv890898	chr8:52579964-52680933	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4873584	PCMTD1	cis	cerebellum	SCAN
rs4873584	PCMTD1	cis	brain	seeQTL
rs4873584	LOC115294	cis	multi-tissue	Pritchard
rs4873584	PCMTD1	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52637400-52650400	Weak transcription	Left Ventricle	heart

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