Variant report

Variant	rs334545
Chromosome Location	chr3:119834921-119834922
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119812799..119816595-chr3:119829619..119835566,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10049256	1.00[CEU][hapmap]
rs10934512	1.00[CEU][hapmap];0.96[GIH][hapmap]
rs1154596	0.87[CEU][hapmap]
rs1154597	0.81[ASW][hapmap];0.87[CEU][hapmap]
rs12152218	1.00[CEU][hapmap]
rs13312998	0.87[CEU][hapmap]
rs1488764	1.00[CEU][hapmap];0.96[GIH][hapmap]
rs1492271	0.87[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap]
rs16830683	0.81[ASW][hapmap];0.87[CEU][hapmap]
rs182839	0.89[ASW][hapmap];0.87[CEU][hapmap];0.86[MKK][hapmap];0.87[AMR][1000 genomes]
rs184576	0.88[EUR][1000 genomes]
rs1907681	1.00[CEU][hapmap]
rs2035671	1.00[CEU][hapmap]
rs2035672	0.80[AMR][1000 genomes]
rs2035673	0.80[AMR][1000 genomes]
rs2035674	1.00[CEU][hapmap];0.96[GIH][hapmap];0.80[AMR][1000 genomes]
rs2130000	1.00[CEU][hapmap]
rs2171599	0.80[AMR][1000 genomes]
rs2319541	1.00[CEU][hapmap]
rs2319543	1.00[CEU][hapmap]
rs28398784	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2874022	1.00[CEU][hapmap]
rs2874023	1.00[CEU][hapmap]
rs3112282	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3112283	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs334534	0.81[ASW][hapmap];0.87[CEU][hapmap];0.87[AMR][1000 genomes]
rs334538	1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[ASN][1000 genomes]
rs334539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs334540	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs334547	0.86[CHB][hapmap]
rs334549	0.89[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs334551	0.80[AMR][1000 genomes]
rs334552	0.87[AMR][1000 genomes]
rs334554	0.87[AMR][1000 genomes]
rs334561	0.87[CEU][hapmap];0.87[AMR][1000 genomes]
rs334565	0.86[MKK][hapmap]
rs4488869	1.00[CEU][hapmap];0.96[GIH][hapmap]
rs4676822	1.00[CEU][hapmap]
rs6438554	0.87[CEU][hapmap]
rs6438558	1.00[CEU][hapmap];0.96[GIH][hapmap];0.85[EUR][1000 genomes]
rs6438559	1.00[CEU][hapmap];0.96[GIH][hapmap]
rs6438564	1.00[CEU][hapmap]
rs6438567	1.00[CEU][hapmap]
rs6764549	1.00[CEU][hapmap]
rs6769988	1.00[CEU][hapmap]
rs6776122	1.00[CEU][hapmap]
rs6781470	1.00[CEU][hapmap];0.96[GIH][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6784239	0.87[CEU][hapmap]
rs6785050	0.87[CEU][hapmap]
rs6794478	1.00[CEU][hapmap]
rs6797689	0.81[ASW][hapmap];0.87[CEU][hapmap]
rs6803611	0.87[CEU][hapmap]
rs6805931	0.87[AMR][1000 genomes]
rs6807868	0.81[ASW][hapmap];0.87[CEU][hapmap]
rs7642171	0.86[CEU][hapmap]
rs7644268	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7650554	0.81[ASW][hapmap];0.87[CEU][hapmap]
rs7653263	1.00[CEU][hapmap]
rs7653396	1.00[CEU][hapmap]
rs787211	0.87[CEU][hapmap]
rs901920	0.82[EUR][1000 genomes]
rs902790	1.00[CEU][hapmap];0.96[GIH][hapmap]
rs902791	1.00[CEU][hapmap]
rs902794	1.00[CEU][hapmap]
rs902795	1.00[CEU][hapmap]
rs923380	0.81[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs923726	1.00[CEU][hapmap]
rs923727	1.00[CEU][hapmap]
rs923728	1.00[CEU][hapmap];0.96[GIH][hapmap]
rs9289143	1.00[CEU][hapmap];0.96[GIH][hapmap]
rs979682	1.00[CEU][hapmap];0.96[GIH][hapmap]
rs9813834	1.00[CEU][hapmap]
rs9841122	1.00[CEU][hapmap]
rs9842302	1.00[CEU][hapmap];0.96[GIH][hapmap]
rs9853082	1.00[CEU][hapmap];0.96[GIH][hapmap]
rs9858566	1.00[CEU][hapmap]

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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs334545	PLA1A	cis	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119822000-119835200	Weak transcription	Psoas Muscle	Psoas
2	chr3:119833200-119836200	Weak transcription	HepG2	liver
3	chr3:119834400-119836200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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