Variant report

Variant	rs10512472
Chromosome Location	chr17:33884804-33884805
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	chr17:33883508..33885797-chr17:33888017..33890924,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267625	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1001441	0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs10068	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs1037590	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1071965	0.90[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs11653310	0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11653357	0.83[AMR][1000 genomes]
rs11870472	0.88[ASN][1000 genomes]
rs12452797	0.90[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12604067	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs12948669	0.83[AMR][1000 genomes]
rs16971217	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap]
rs17637907	0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1968578	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225247	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs225251	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs225254	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs225262	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs225277	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs225306	0.80[CHD][hapmap];0.85[JPT][hapmap]
rs2840044	0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs28498569	0.90[ASN][1000 genomes]
rs2889311	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34054049	0.90[ASN][1000 genomes]
rs7503168	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9891800	0.81[ASN][1000 genomes]
rs9894057	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9897552	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap]
rs9900378	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs9902765	0.83[AMR][1000 genomes]
rs9905788	0.90[ASN][1000 genomes]
rs9906105	0.90[ASN][1000 genomes]
rs9908158	0.83[ASN][1000 genomes]
rs9913003	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
2	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer 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	44 gene(s)	inside rSNPs	diseases
3	nsv1060890	chr17:33884124-34011034	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv543318	chr17:33884124-34011034	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Platelet counts	22139419	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10512472	AP2B1	cis	cerebellum	SCAN
rs10512472	PEX12	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33870400-33888600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr17:33883200-33886000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:33883200-33886400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr17:33883400-33888600	Enhancers	Primary hematopoietic stem cells	blood
5	chr17:33883800-33886400	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr17:33884600-33885200	Flanking Active TSS	K562	blood

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