Variant report

Variant	rs899981
Chromosome Location	chr15:73935329-73935330
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	chr15:73924609..73926509-chr15:73934270..73937207,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156642	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11072427	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072428	0.81[TSI][hapmap]
rs11072434	0.82[MEX][hapmap]
rs11574495	0.82[JPT][hapmap]
rs11852484	0.83[JPT][hapmap]
rs12148532	0.87[TSI][hapmap]
rs12594627	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1383616	0.81[TSI][hapmap]
rs1542579	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1542580	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17185294	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs17185525	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2509	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs56712926	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58443257	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59104311	0.80[ASN][1000 genomes]
rs60696711	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62004587	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62004592	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62004612	0.82[AMR][1000 genomes]
rs67776653	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs710086	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7182124	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72625789	0.87[ASN][1000 genomes]
rs72625790	0.86[ASN][1000 genomes]
rs8041181	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs8041523	0.82[CHB][hapmap];0.86[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037540	chr15:73712637-73982420	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs899981	PML	cis	parietal	SCAN
rs899981	ARIH1	cis	cerebellum	SCAN
rs899981	SIN3A	cis	cerebellum	SCAN
rs899981	TLE3	cis	parietal	SCAN
rs899981	GPER	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73929800-73940000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr15:73932800-73940000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:73935000-73942600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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