Variant report

Variant	rs1513390
Chromosome Location	chr11:85778212-85778213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85777862..85782517-chr11:85902953..85907117,7	K562	blood:
2	chr11:85762145..85764012-chr11:85775530..85778515,2	MCF-7	breast:
3	chr11:85775759..85778337-chr11:85946507..85948966,2	K562	blood:
4	chr11:85777613..85779619-chr11:85854927..85856671,2	K562	blood:
5	chr11:85778125..85779781-chr11:85819659..85821681,2	K562	blood:
6	chr11:85776467..85780584-chr11:85902948..85906650,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254502	Chromatin interaction
ENSG00000254699	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1996108	0.83[ASN][1000 genomes]
rs2155051	0.80[ASN][1000 genomes]
rs2458493	0.90[ASN][1000 genomes]
rs2458500	0.94[ASN][1000 genomes]
rs2508688	0.80[ASN][1000 genomes]
rs2509608	0.94[ASN][1000 genomes]
rs2509609	0.93[ASN][1000 genomes]
rs489486	0.89[ASN][1000 genomes]
rs497711	0.92[ASN][1000 genomes]
rs528109	0.81[ASN][1000 genomes]
rs540422	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs542167	0.80[ASN][1000 genomes]
rs544458	0.99[ASN][1000 genomes]
rs544848	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs547767	0.82[ASN][1000 genomes]
rs564658	0.85[EUR][1000 genomes]
rs583126	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs588380	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs592297	0.80[ASN][1000 genomes]
rs596864	0.81[EUR][1000 genomes]
rs597446	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs604767	0.89[AFR][1000 genomes]
rs613222	0.89[AFR][1000 genomes]
rs617836	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs618001	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs622220	0.84[ASN][1000 genomes]
rs627818	0.81[ASN][1000 genomes]
rs634719	0.95[ASN][1000 genomes]
rs635168	0.90[ASN][1000 genomes]
rs655641	0.83[ASN][1000 genomes]
rs664050	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs669556	0.93[ASN][1000 genomes]
rs680119	0.82[ASN][1000 genomes]
rs683340	0.83[EUR][1000 genomes]
rs9804630	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035489	chr11:85502953-85778229	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
rs1513390	PICALM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85773600-85778800	Weak transcription	Spleen	Spleen
2	chr11:85773600-85781000	Active TSS	Right Ventricle	heart
3	chr11:85773800-85780600	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr11:85773800-85780600	Active TSS	GM12878-XiMat	blood
5	chr11:85775000-85780600	Active TSS	Stomach Smooth Muscle	stomach
6	chr11:85775200-85779200	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr11:85775600-85778400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:85775600-85780800	Active TSS	Ovary	ovary
9	chr11:85775600-85781000	Active TSS	Hela-S3	cervix
10	chr11:85775800-85780600	Active TSS	HSMMtube	muscle
11	chr11:85776000-85778400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:85776000-85781200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr11:85776200-85778400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr11:85776200-85778400	Weak transcription	Esophagus	oesophagus
15	chr11:85776200-85779200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:85776200-85780600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:85776200-85780600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:85776200-85780800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:85776200-85780800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:85776400-85778400	Weak transcription	Small Intestine	intestine
21	chr11:85776400-85779800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr11:85776400-85780600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr11:85776400-85780600	Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr11:85776400-85780600	Active TSS	HMEC	breast
25	chr11:85776400-85780800	Active TSS	Right Atrium	heart
26	chr11:85776400-85781000	Active TSS	HSMM	muscle
27	chr11:85776400-85781000	Active TSS	NHLF	lung
28	chr11:85776400-85781200	Active TSS	Psoas Muscle	Psoas
29	chr11:85776600-85778800	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr11:85776600-85779000	Flanking Active TSS	Dnd41	blood
31	chr11:85776600-85779200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr11:85776600-85780400	Active TSS	Primary T cells fromperipheralblood	blood
33	chr11:85776600-85780400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
34	chr11:85776600-85780400	Active TSS	Fetal Muscle Leg	muscle
35	chr11:85776600-85780800	Active TSS	Aorta	Aorta
36	chr11:85776600-85781000	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr11:85776800-85779200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr11:85776800-85780600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr11:85776800-85780600	Active TSS	Brain Substantia Nigra	brain
40	chr11:85776800-85780600	Active TSS	Thymus	Thymus
41	chr11:85776800-85780600	Active TSS	NHEK	skin
42	chr11:85776800-85780800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr11:85776800-85780800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:85776800-85780800	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr11:85776800-85781000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr11:85777000-85779400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:85777000-85780400	Active TSS	Primary monocytes fromperipheralblood	blood
48	chr11:85777000-85780600	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr11:85777000-85780600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:85777000-85780600	Active TSS	Fetal Intestine Large	intestine

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