Variant report

Variant	rs541458
Chromosome Location	chr11:85788351-85788352
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	chr11:85780388..85781944-chr11:85788305..85790883,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073921	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1973630	0.84[EUR][1000 genomes]
rs2155051	0.84[ASW][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap]
rs2508691	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2508696	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs480781	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs493254	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs535590	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs536841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs544458	0.94[AFR][1000 genomes]
rs561646	0.96[CEU][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs561655	0.84[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs565719	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs587038	0.89[EUR][1000 genomes]
rs602222	0.95[CEU][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs604767	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs606505	0.89[EUR][1000 genomes]
rs609903	0.84[ASW][hapmap];0.96[CEU][hapmap];0.90[GIH][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs622220	0.88[YRI][hapmap]
rs627818	0.92[ASW][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.94[YRI][hapmap]
rs631639	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs634719	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs636355	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs638509	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs639012	0.84[EUR][1000 genomes]
rs645299	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs652165	0.99[ASN][1000 genomes]
rs659023	0.84[GIH][hapmap]
rs659863	0.92[EUR][1000 genomes]
rs669813	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs673751	0.87[EUR][1000 genomes]
rs676733	0.92[CEU][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs677869	0.92[EUR][1000 genomes]
rs677909	0.96[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs682928	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs694011	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs867611	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]

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	esv1829985	chr11:85740319-85789350	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1050948	chr11:85756325-85968665	Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv541117	chr11:85756325-85968665	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs541458	PICALM	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85781400-85796000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:85785600-85788600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr11:85785800-85788400	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr11:85785800-85789800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:85788200-85789800	Enhancers	Primary monocytes fromperipheralblood	blood

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