Variant report

Variant	rs1214669
Chromosome Location	chr11:85784268-85784269
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85779081..85782313-chr11:85782461..85788148,6	MCF-7	breast:
2	chr11:85783105..85786132-chr11:85791700..85793903,3	MCF-7	breast:
3	chr11:85773042..85775318-chr11:85782824..85785081,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073921	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1237999	0.82[ASN][1000 genomes]
rs12808312	0.84[EUR][1000 genomes]
rs1949221	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1973630	0.83[ASN][1000 genomes]
rs2508381	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2508690	0.87[EUR][1000 genomes]
rs2508691	0.87[ASN][1000 genomes]
rs2508692	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2508693	0.85[ASN][1000 genomes]
rs2508696	0.82[ASN][1000 genomes]
rs2508697	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3016240	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3016786	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs472486	0.81[ASN][1000 genomes]
rs475639	0.84[EUR][1000 genomes]
rs484154	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs493254	0.87[ASN][1000 genomes]
rs497816	0.85[ASN][1000 genomes]
rs501505	0.81[EUR][1000 genomes]
rs519778	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs526904	0.84[ASN][1000 genomes]
rs532470	0.88[EUR][1000 genomes]
rs541674	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs542126	0.85[ASN][1000 genomes]
rs545592	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs553141	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs561646	0.86[ASN][1000 genomes]
rs563773	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs565031	0.83[EUR][1000 genomes]
rs566975	0.84[ASN][1000 genomes]
rs572979	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs580887	0.81[ASN][1000 genomes]
rs583162	0.85[ASN][1000 genomes]
rs586274	0.80[ASN][1000 genomes]
rs587038	0.80[ASN][1000 genomes]
rs602222	0.82[ASN][1000 genomes]
rs604767	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs606505	0.80[ASN][1000 genomes]
rs609903	0.84[ASN][1000 genomes]
rs613222	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs629343	0.85[ASN][1000 genomes]
rs636355	0.84[ASN][1000 genomes]
rs638509	0.85[AMR][1000 genomes]
rs642949	0.81[ASN][1000 genomes]
rs645293	0.80[ASN][1000 genomes]
rs645299	0.82[ASN][1000 genomes]
rs647422	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs652165	0.82[AMR][1000 genomes]
rs659863	0.90[ASN][1000 genomes]
rs666682	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs669813	0.87[ASN][1000 genomes]
rs676733	0.84[ASN][1000 genomes]
rs677869	0.90[ASN][1000 genomes]
rs677909	0.90[ASN][1000 genomes]
rs682928	0.81[ASN][1000 genomes]
rs683494	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs694011	0.92[ASN][1000 genomes]
rs867611	0.90[ASN][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
rs1214669	PICALM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85780800-85784800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:85781400-85796000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:85781600-85784400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:85781800-85785600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:85782000-85784800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr11:85782400-85785200	Weak transcription	Placenta	Placenta
7	chr11:85783600-85785000	Weak transcription	HSMM	muscle
8	chr11:85783800-85785000	Weak transcription	K562	blood

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