Variant report

Variant	rs4780216
Chromosome Location	chr15:34401353-34401354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:34401088..34402962-chr15:34501811..34503818,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134152	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11072954	0.95[EUR][1000 genomes]
rs11634597	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11853879	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11856158	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12592547	1.00[CEU][hapmap];0.83[GIH][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs12592856	0.88[EUR][1000 genomes]
rs12594048	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs12903028	0.88[EUR][1000 genomes]
rs1436923	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[MKK][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16958770	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1865925	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2339374	0.88[EUR][1000 genomes]
rs2568532	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2576308	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2576310	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28376576	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794593	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4288968	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4468578	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4780214	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4780215	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs522397	0.90[JPT][hapmap]
rs56310728	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57205845	0.80[ASN][1000 genomes]
rs623941	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs6495519	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7161835	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7163226	0.99[EUR][1000 genomes]
rs7181861	0.83[TSI][hapmap]
rs7182085	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721122	1.00[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73374335	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8028703	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8038259	1.00[CEU][hapmap];0.96[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	nsv456789	chr15:34034421-34426618	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv568920	chr15:34034421-34426618	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv471235	chr15:34035529-34421951	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1035579	chr15:34363159-34501115	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv903986	chr15:34394273-34421951	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4780216	PGBD4	cis	multi-tissue	Pritchard
rs4780216	PGBD4	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34395000-34402200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:34395000-34407200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr15:34395200-34401400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:34395400-34401600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr15:34395400-34402000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr15:34395400-34403600	Weak transcription	Psoas Muscle	Psoas
7	chr15:34395400-34408400	Weak transcription	HSMMtube	muscle
8	chr15:34395600-34402200	Weak transcription	K562	blood
9	chr15:34395600-34403600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:34395600-34408200	Weak transcription	Fetal Muscle Leg	muscle
11	chr15:34395800-34401400	Weak transcription	HepG2	liver
12	chr15:34396000-34407200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr15:34397800-34403800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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