Variant report

Variant	rs12277986
Chromosome Location	chr11:85820203-85820204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85812308..85815576-chr11:85816844..85820250,5	K562	blood:
2	chr11:85752580..85755769-chr11:85817812..85820593,3	K562	blood:
3	chr11:85818918..85820717-chr11:85851486..85854070,2	K562	blood:
4	chr11:85816871..85820639-chr11:85825942..85829677,4	K562	blood:
5	chr11:85778125..85779781-chr11:85819659..85821681,2	K562	blood:
6	chr11:85752580..85754495-chr11:85817812..85820593,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10128700	0.81[EUR][1000 genomes]
rs11234544	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11234548	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12270433	0.82[EUR][1000 genomes]
rs12271390	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12276435	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12281494	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12282655	0.87[EUR][1000 genomes]
rs12284629	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12292364	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12294130	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17159904	0.81[EUR][1000 genomes]
rs17745248	0.81[EUR][1000 genomes]
rs17745273	0.81[EUR][1000 genomes]
rs17745474	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17817919	0.80[EUR][1000 genomes]
rs17817956	0.84[EUR][1000 genomes]
rs2001241	0.87[EUR][1000 genomes]
rs4943937	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4944555	0.83[EUR][1000 genomes]
rs4944556	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55791429	0.84[EUR][1000 genomes]
rs55815523	0.81[EUR][1000 genomes]
rs56187740	0.83[EUR][1000 genomes]
rs56207019	0.82[EUR][1000 genomes]
rs7128598	0.82[EUR][1000 genomes]
rs72950443	0.86[EUR][1000 genomes]
rs72950453	0.87[EUR][1000 genomes]
rs72950456	0.87[EUR][1000 genomes]
rs72959906	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72959929	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72965157	0.82[EUR][1000 genomes]
rs72965166	0.86[EUR][1000 genomes]
rs7943152	0.84[AMR][1000 genomes];0.91[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	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
3	esv3332891	chr11:85819854-85823752	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12277986	PICALM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85813600-85826600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:85819800-85820400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr11:85819800-85820800	Flanking Active TSS	K562	blood
4	chr11:85820000-85820600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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