Variant report

Variant	rs9307305
Chromosome Location	chr4:106442518-106442519
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:106442078..106442580-chr4:106636518..106637073,2	K562	blood:
2	chr4:106441385..106442611-chr4:106587453..106588510,4	MCF-7	breast:
3	chr4:106441991..106443723-chr4:106514894..106517576,2	MCF-7	breast:
4	chr4:106441496..106442694-chr4:106586959..106588547,10	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10020998	0.82[CEU][hapmap]
rs10024331	0.82[CEU][hapmap]
rs10026456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1125254	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs1388040	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1490599	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1490600	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1490601	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1490602	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17584200	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2023840	0.82[CEU][hapmap]
rs2046880	0.82[CEU][hapmap]
rs2189228	0.81[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2866798	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2866799	0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3796916	0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3796917	0.89[JPT][hapmap]
rs3864225	0.82[CEU][hapmap]
rs3960769	0.94[JPT][hapmap];0.88[MEX][hapmap]
rs3974414	0.81[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4235414	0.82[CEU][hapmap]
rs4699176	0.82[CEU][hapmap]
rs4699186	0.89[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4699187	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6533199	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs6533202	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6533204	0.89[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6533205	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6816997	0.82[CEU][hapmap]
rs6817760	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6853877	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs763289	0.82[CEU][hapmap]
rs7666509	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7672413	0.81[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs7686705	0.81[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7695462	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9307304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999896	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv275355	chr4:106442212-106442586	Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv521423	chr4:106442518-106448900	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9307305	PPA2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106442000-106442600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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