Variant report

Variant	rs12808312
Chromosome Location	chr11:85736374-85736375
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:85729904-85736468	K562	blood:	n/a	n/a

Variant related genes	Relation type
PICALM	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1214669	0.84[EUR][1000 genomes]
rs1949221	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2508381	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2508690	0.91[EUR][1000 genomes]
rs2508692	0.89[EUR][1000 genomes]
rs2508693	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2508696	0.82[ASN][1000 genomes]
rs2508697	0.84[EUR][1000 genomes]
rs3016240	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3016786	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs475639	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs478711	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs484154	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs501505	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs519778	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs529904	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs532470	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs541674	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs545592	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs553141	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs561646	0.83[ASN][1000 genomes]
rs563773	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs565031	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs572979	0.83[EUR][1000 genomes]
rs579406	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs587038	0.81[ASN][1000 genomes]
rs602222	0.82[ASN][1000 genomes]
rs604767	0.87[EUR][1000 genomes]
rs606505	0.81[ASN][1000 genomes]
rs609903	0.85[ASN][1000 genomes]
rs613222	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs617836	0.86[AFR][1000 genomes]
rs618001	0.80[AFR][1000 genomes]
rs636355	0.85[ASN][1000 genomes]
rs636772	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs642949	0.83[ASN][1000 genomes]
rs645299	0.82[ASN][1000 genomes]
rs647422	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs664050	0.80[AFR][1000 genomes]
rs666682	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs671686	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs676733	0.85[ASN][1000 genomes]
rs682928	0.80[ASN][1000 genomes]
rs683494	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv1048818	chr11:85524635-85746473	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv541116	chr11:85524635-85746473	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1053808	chr11:85588919-85757693	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv468769	chr11:85683554-85757589	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv555641	chr11:85683554-85757589	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv898054	chr11:85683554-85772636	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv468770	chr11:85688209-85751883	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv555642	chr11:85688209-85751883	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv468771	chr11:85688209-85757589	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv468773	chr11:85688209-85757589	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv555643	chr11:85688209-85757589	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv468774	chr11:85688209-85775059	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv555644	chr11:85688209-85775059	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12808312	PICALM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85659400-85745800	Weak transcription	Stomach Mucosa	stomach
2	chr11:85663800-85740200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:85665200-85742600	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr11:85665200-85743000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr11:85675000-85742600	Strong transcription	Primary B cells from peripheral blood	blood
6	chr11:85697800-85742600	Strong transcription	HUVEC	blood vessel
7	chr11:85700600-85742400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr11:85701000-85745000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:85703200-85742800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:85712800-85740800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:85712800-85741600	Weak transcription	Aorta	Aorta
12	chr11:85712800-85743400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr11:85716600-85741400	Weak transcription	Fetal Heart	heart
14	chr11:85716800-85746200	Weak transcription	Pancreas	Pancrea
15	chr11:85717600-85739800	Weak transcription	Psoas Muscle	Psoas
16	chr11:85718000-85738400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr11:85719800-85736800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr11:85719800-85743400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:85720400-85742600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:85720800-85742600	Strong transcription	HSMM	muscle
21	chr11:85721800-85738600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr11:85721800-85745800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr11:85725200-85736800	Weak transcription	Colonic Mucosa	Colon
24	chr11:85725600-85742800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr11:85726200-85736800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr11:85727200-85741800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:85727200-85742000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr11:85727800-85741800	Strong transcription	Liver	Liver
29	chr11:85727800-85745800	Weak transcription	Right Ventricle	heart
30	chr11:85728000-85736800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr11:85728600-85742000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr11:85728800-85736800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr11:85729800-85742600	Strong transcription	Osteobl	bone
34	chr11:85730000-85742000	Strong transcription	NHDF-Ad	bronchial
35	chr11:85730000-85742400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:85730000-85742400	Strong transcription	Fetal Thymus	thymus
37	chr11:85730000-85742600	Strong transcription	Placenta	Placenta
38	chr11:85730200-85738200	Strong transcription	NH-A	brain
39	chr11:85730200-85742600	Strong transcription	Fetal Lung	lung
40	chr11:85730600-85743200	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr11:85730800-85742200	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr11:85730800-85742600	Strong transcription	Dnd41	blood
43	chr11:85731600-85740000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr11:85731600-85754200	Weak transcription	Brain Germinal Matrix	brain
45	chr11:85731800-85736800	Weak transcription	Brain Anterior Caudate	brain
46	chr11:85732200-85744600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr11:85732600-85742400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr11:85732600-85743000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:85732800-85736800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr11:85732800-85742600	Strong transcription	Primary neutrophils fromperipheralblood	blood

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