Variant report

Variant	rs617836
Chromosome Location	chr11:85734936-85734937
allele	A/T
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	chr11:85734647-85734942	K562	blood:	n/a	n/a
2	MAFF	chr11:85734650-85734947	K562	blood:	n/a	n/a
3	POLR2A	chr11:85734918-85734937	K562	blood:	n/a	n/a
4	POLR2A	chr11:85729904-85736468	K562	blood:	n/a	n/a
5	SPI1	chr11:85734679-85734977	HL-60	blood:	n/a	chr11:85734777-85734786
6	IRF1	chr11:85734613-85734937	K562	blood:	n/a	chr11:85734777-85734787 chr11:85734777-85734791 chr11:85734776-85734785

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85725973..85728229-chr11:85733987..85735840,2	K562	blood:
2	chr11:85734003..85736029-chr11:85992603..85995155,2	K562	blood:

Variant related genes	Relation type
PICALM	TF binding region
ENSG00000254783	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs12808312	0.86[AFR][1000 genomes]
rs1513390	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1996108	0.98[ASN][1000 genomes]
rs2077815	0.91[ASN][1000 genomes]
rs2155051	0.95[ASN][1000 genomes]
rs2458496	0.91[ASN][1000 genomes]
rs2458499	0.82[ASN][1000 genomes]
rs2458500	0.80[ASN][1000 genomes]
rs2508688	0.95[ASN][1000 genomes]
rs2509608	0.80[ASN][1000 genomes]
rs472618	0.87[ASN][1000 genomes]
rs475639	0.82[AFR][1000 genomes]
rs488134	0.90[ASN][1000 genomes]
rs489486	0.84[ASN][1000 genomes]
rs494369	0.94[ASN][1000 genomes]
rs497711	0.89[ASN][1000 genomes]
rs504129	0.88[ASN][1000 genomes]
rs527162	0.90[ASN][1000 genomes]
rs528109	0.96[ASN][1000 genomes]
rs540422	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs541674	0.93[AFR][1000 genomes]
rs542167	0.95[ASN][1000 genomes]
rs544458	0.84[ASN][1000 genomes]
rs544848	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs547767	0.91[ASN][1000 genomes]
rs548121	0.85[ASN][1000 genomes]
rs564658	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs583126	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs585820	0.91[ASN][1000 genomes]
rs588076	0.94[ASN][1000 genomes]
rs588380	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs592297	0.94[ASN][1000 genomes]
rs592314	0.86[ASN][1000 genomes]
rs595972	0.91[ASN][1000 genomes]
rs596864	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs597446	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs600258	0.94[ASN][1000 genomes]
rs600743	0.89[ASN][1000 genomes]
rs601185	0.94[ASN][1000 genomes]
rs602391	0.87[ASN][1000 genomes]
rs603615	0.95[ASN][1000 genomes]
rs616555	0.90[ASN][1000 genomes]
rs618001	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs618629	0.94[ASN][1000 genomes]
rs618679	0.84[ASN][1000 genomes]
rs622220	0.99[ASN][1000 genomes]
rs626542	0.88[ASN][1000 genomes]
rs627818	0.96[ASN][1000 genomes]
rs634719	0.86[ASN][1000 genomes]
rs635168	0.82[ASN][1000 genomes]
rs637304	0.90[ASN][1000 genomes]
rs648270	0.93[ASN][1000 genomes]
rs654194	0.91[ASN][1000 genomes]
rs655641	0.98[ASN][1000 genomes]
rs659801	0.82[ASN][1000 genomes]
rs664050	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs666682	0.87[AFR][1000 genomes]
rs670606	0.91[ASN][1000 genomes]
rs680119	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs682366	0.90[ASN][1000 genomes]
rs683340	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7938033	0.83[ASN][1000 genomes]
rs7951988	0.90[ASN][1000 genomes]
rs9804630	0.86[ASN][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
rs617836	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	chr11:85666000-85735800	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr11:85675000-85742600	Strong transcription	Primary B cells from peripheral blood	blood
7	chr11:85697800-85742600	Strong transcription	HUVEC	blood vessel
8	chr11:85700600-85742400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr11:85701000-85745000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:85703200-85742800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:85712600-85736200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:85712800-85735800	Weak transcription	Esophagus	oesophagus
13	chr11:85712800-85740800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:85712800-85741600	Weak transcription	Aorta	Aorta
15	chr11:85712800-85743400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr11:85714000-85735600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:85716600-85741400	Weak transcription	Fetal Heart	heart
18	chr11:85716800-85736200	Weak transcription	Lung	lung
19	chr11:85716800-85746200	Weak transcription	Pancreas	Pancrea
20	chr11:85717600-85739800	Weak transcription	Psoas Muscle	Psoas
21	chr11:85718000-85738400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr11:85718200-85736200	Weak transcription	Gastric	stomach
23	chr11:85719800-85736800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr11:85719800-85743400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:85720200-85735600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr11:85720400-85742600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr11:85720800-85736000	Weak transcription	Spleen	Spleen
28	chr11:85720800-85742600	Strong transcription	HSMM	muscle
29	chr11:85721800-85736200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr11:85721800-85738600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr11:85721800-85745800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr11:85725200-85736800	Weak transcription	Colonic Mucosa	Colon
33	chr11:85725600-85742800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr11:85726200-85736800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr11:85727200-85736200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr11:85727200-85741800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr11:85727200-85742000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr11:85727600-85735600	Weak transcription	Brain Angular Gyrus	brain
39	chr11:85727800-85735800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr11:85727800-85741800	Strong transcription	Liver	Liver
41	chr11:85727800-85745800	Weak transcription	Right Ventricle	heart
42	chr11:85728000-85735600	Weak transcription	HSMMtube	muscle
43	chr11:85728000-85736800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr11:85728600-85742000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr11:85728800-85736800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr11:85729000-85735600	Weak transcription	Brain Substantia Nigra	brain
47	chr11:85729800-85742600	Strong transcription	Osteobl	bone
48	chr11:85730000-85742000	Strong transcription	NHDF-Ad	bronchial
49	chr11:85730000-85742400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr11:85730000-85742400	Strong transcription	Fetal Thymus	thymus

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