Variant report

Variant	rs28606601
Chromosome Location	chr19:39612084-39612085
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr19:39612064-39612123	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39610539..39613482-chr19:39683239..39685361,3	MCF-7	breast:
2	chr19:39611154..39613169-chr19:39902607..39904497,2	MCF-7	breast:

Variant related genes	Relation type
PAK4	TF binding region
ENSG00000090924	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11882372	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1313617	0.85[EUR][1000 genomes]
rs2569368	0.83[EUR][1000 genomes]
rs2569369	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs516004	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs563873	0.85[EUR][1000 genomes]
rs565812	0.85[EUR][1000 genomes]
rs62119549	0.82[EUR][1000 genomes]
rs62120479	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62120480	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62120481	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62120482	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62120483	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62120484	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62120485	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62120486	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62120488	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62120489	0.91[EUR][1000 genomes]
rs62120490	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs692346	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs692438	0.85[EUR][1000 genomes]
rs692461	0.85[EUR][1000 genomes]
rs692730	0.84[EUR][1000 genomes]
rs7256505	0.90[EUR][1000 genomes]
rs7256546	0.90[EUR][1000 genomes]
rs774913	0.85[EUR][1000 genomes]
rs774915	0.84[EUR][1000 genomes]
rs774916	0.84[EUR][1000 genomes]
rs774917	0.84[EUR][1000 genomes]
rs774918	0.84[EUR][1000 genomes]
rs774919	0.84[EUR][1000 genomes]
rs774920	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1067028	chr19:39567228-39622846	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1060469	chr19:39567228-39624790	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39603200-39614600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:39603600-39612600	Weak transcription	Hela-S3	cervix
3	chr19:39611000-39616000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:39611600-39613800	Enhancers	A549	lung
5	chr19:39611800-39613000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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