Variant report

Variant	rs572979
Chromosome Location	chr11:85803276-85803277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10792830	0.82[ASN][1000 genomes]
rs1214669	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1237999	0.88[ASN][1000 genomes]
rs12808312	0.83[EUR][1000 genomes]
rs1949221	0.85[EUR][1000 genomes]
rs2508381	0.81[EUR][1000 genomes]
rs2508690	0.80[EUR][1000 genomes]
rs2508691	0.82[ASN][1000 genomes]
rs2508692	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2508693	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2508697	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3016240	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3016786	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs471470	0.82[ASN][1000 genomes]
rs472486	0.86[ASN][1000 genomes]
rs474479	0.81[ASN][1000 genomes]
rs475639	0.84[EUR][1000 genomes]
rs484154	0.80[EUR][1000 genomes]
rs493254	0.82[ASN][1000 genomes]
rs497816	0.90[ASN][1000 genomes]
rs501505	0.81[EUR][1000 genomes]
rs519778	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs519961	0.81[ASN][1000 genomes]
rs526904	0.89[ASN][1000 genomes]
rs541674	0.85[EUR][1000 genomes]
rs542126	0.90[ASN][1000 genomes]
rs543293	0.82[ASN][1000 genomes]
rs545592	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs553141	0.81[EUR][1000 genomes]
rs561646	0.81[ASN][1000 genomes]
rs563773	0.80[EUR][1000 genomes]
rs565031	0.83[EUR][1000 genomes]
rs566975	0.89[ASN][1000 genomes]
rs573167	0.82[ASN][1000 genomes]
rs580887	0.86[ASN][1000 genomes]
rs583162	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs586274	0.86[ASN][1000 genomes]
rs604767	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs613222	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs629343	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs645293	0.86[ASN][1000 genomes]
rs647422	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs659023	0.85[ASN][1000 genomes]
rs659863	0.85[ASN][1000 genomes]
rs666682	0.86[EUR][1000 genomes]
rs669813	0.82[ASN][1000 genomes]
rs677869	0.85[ASN][1000 genomes]
rs677909	0.85[ASN][1000 genomes]
rs683494	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs694011	0.86[ASN][1000 genomes]
rs7114331	0.81[ASN][1000 genomes]
rs867611	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
rs572979	PICALM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85798400-85803800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr11:85801400-85804000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:85802000-85803400	Enhancers	Osteobl	bone
4	chr11:85802200-85803400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr11:85802400-85803400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr11:85802600-85803400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:85802600-85803400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr11:85802600-85803600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr11:85802800-85803400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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