Variant report

Variant	rs12281494
Chromosome Location	chr11:85799241-85799242
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85798893..85802407-chr11:85803626..85806353,3	K562	blood:
2	chr11:85796338..85798988-chr11:85799126..85803247,4	K562	blood:

Variant related genes	Relation type
ENSG00000238666	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10128700	0.88[EUR][1000 genomes]
rs10501603	0.82[EUR][1000 genomes]
rs10501605	0.87[EUR][1000 genomes]
rs10501607	0.87[EUR][1000 genomes]
rs11234489	0.80[EUR][1000 genomes]
rs11234492	0.81[EUR][1000 genomes]
rs11234496	0.82[EUR][1000 genomes]
rs11234502	0.83[EUR][1000 genomes]
rs11234512	0.83[EUR][1000 genomes]
rs11234513	0.83[EUR][1000 genomes]
rs11234517	0.83[EUR][1000 genomes]
rs11234544	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11234548	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12270433	0.89[EUR][1000 genomes]
rs12271390	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12276435	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12277986	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12279956	0.83[EUR][1000 genomes]
rs12281958	0.83[EUR][1000 genomes]
rs12282655	0.94[EUR][1000 genomes]
rs12284629	0.91[EUR][1000 genomes]
rs12287170	0.83[EUR][1000 genomes]
rs12292364	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12294130	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17159904	0.90[EUR][1000 genomes]
rs17744938	0.82[EUR][1000 genomes]
rs17745105	0.83[EUR][1000 genomes]
rs17745153	0.83[EUR][1000 genomes]
rs17745236	0.86[EUR][1000 genomes]
rs17745248	0.88[EUR][1000 genomes]
rs17745273	0.88[EUR][1000 genomes]
rs17745474	0.87[EUR][1000 genomes]
rs17817582	0.82[EUR][1000 genomes]
rs17817588	0.81[EUR][1000 genomes]
rs17817690	0.83[EUR][1000 genomes]
rs17817859	0.85[EUR][1000 genomes]
rs17817883	0.87[EUR][1000 genomes]
rs17817919	0.87[EUR][1000 genomes]
rs17817956	0.91[EUR][1000 genomes]
rs2001241	0.94[EUR][1000 genomes]
rs2084077	0.81[EUR][1000 genomes]
rs4943934	0.85[EUR][1000 genomes]
rs4943937	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4944550	0.83[EUR][1000 genomes]
rs4944552	0.83[EUR][1000 genomes]
rs4944553	0.83[EUR][1000 genomes]
rs4944554	0.86[EUR][1000 genomes]
rs4944555	0.90[EUR][1000 genomes]
rs4944556	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55697624	0.80[EUR][1000 genomes]
rs55791429	0.91[EUR][1000 genomes]
rs55815523	0.88[EUR][1000 genomes]
rs56026701	0.85[EUR][1000 genomes]
rs56187740	0.90[EUR][1000 genomes]
rs56207019	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57125313	0.80[EUR][1000 genomes]
rs58937798	0.85[EUR][1000 genomes]
rs7128598	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72949443	0.83[EUR][1000 genomes]
rs72950443	0.93[EUR][1000 genomes]
rs72950453	0.94[EUR][1000 genomes]
rs72950456	0.94[EUR][1000 genomes]
rs72951266	0.83[EUR][1000 genomes]
rs72951268	0.82[EUR][1000 genomes]
rs72959177	0.83[EUR][1000 genomes]
rs72959197	0.83[EUR][1000 genomes]
rs72959906	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72959929	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72961110	0.84[EUR][1000 genomes]
rs72963077	0.83[EUR][1000 genomes]
rs72963086	0.84[EUR][1000 genomes]
rs72963092	0.87[EUR][1000 genomes]
rs72965157	0.89[EUR][1000 genomes]
rs72965166	0.93[EUR][1000 genomes]
rs7943152	0.88[AMR][1000 genomes];1.00[EUR][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
rs12281494	PICALM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85791600-85801200	Weak transcription	Pancreas	Pancrea
2	chr11:85796200-85801200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:85798400-85803800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr11:85798600-85800000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr11:85798600-85800200	Weak transcription	NH-A	brain
6	chr11:85798800-85802600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:85798800-85802600	Weak transcription	HSMMtube	muscle
8	chr11:85799000-85800800	Weak transcription	HSMM	muscle
9	chr11:85799200-85799600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:85799200-85799600	Enhancers	Placenta	Placenta

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