Variant report

Variant	rs548076
Chromosome Location	chr11:86890088-86890089
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	chr11:86889371..86892096-chr11:86895507..86898091,3	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11234978	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11822478	0.80[ASN][1000 genomes]
rs11824454	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11825467	0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2847352	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34782550	0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34806361	0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4578415	1.00[JPT][hapmap]
rs476642	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482944	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs485113	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489073	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs493708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs498059	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs498407	0.80[ASN][1000 genomes]
rs500725	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs513938	1.00[JPT][hapmap]
rs520718	0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs541345	0.81[GIH][hapmap]
rs542279	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs545265	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs556724	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs56338039	0.80[ASN][1000 genomes]
rs570898	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs572253	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs578116	0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs587063	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs605658	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs618159	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61904178	0.80[ASN][1000 genomes]
rs61904179	0.80[ASN][1000 genomes]
rs61904181	0.80[ASN][1000 genomes]
rs61904207	0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61906205	0.80[ASN][1000 genomes]
rs631930	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs638771	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs654152	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs654451	1.00[CEU][hapmap]
rs668768	0.80[ASN][1000 genomes]
rs693653	0.80[ASN][1000 genomes]
rs7950416	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037042	chr11:86586876-86978492	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv541119	chr11:86586876-86978492	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv898059	chr11:86754948-86949369	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1043562	chr11:86755535-87547185	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv541120	chr11:86755535-87547185	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1046288	chr11:86757573-87158571	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv1045057	chr11:86794670-87033779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv541121	chr11:86794670-87033779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv468777	chr11:86794856-86985581	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv555707	chr11:86794856-86985581	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv898060	chr11:86822077-86912633	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv420	chr11:86845328-86890111	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv898061	chr11:86850483-86944982	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv468778	chr11:86850483-86974576	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv555708	chr11:86850483-86974576	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv898062	chr11:86864277-86902079	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv898063	chr11:86864277-86944982	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv898064	chr11:86864277-87013438	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	esv2829956	chr11:86872504-87025059	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv518332	chr11:86889284-86891077	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv525787	chr11:86889284-86920178	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs548076	PICALM	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86880600-86891800	Weak transcription	Aorta	Aorta
2	chr11:86880800-86892600	Weak transcription	Liver	Liver
3	chr11:86881800-86891000	Weak transcription	Thymus	Thymus
4	chr11:86882000-86928000	Weak transcription	Left Ventricle	heart
5	chr11:86884400-86891400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr11:86884600-86896600	Weak transcription	Fetal Kidney	kidney
7	chr11:86884600-86899200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr11:86884800-86901200	Weak transcription	K562	blood
9	chr11:86885000-86892000	Weak transcription	Brain Substantia Nigra	brain
10	chr11:86885000-86893200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:86885000-86902200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr11:86885200-86890800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr11:86885200-86891800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:86885400-86891600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:86885800-86891800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr11:86886200-86894800	Weak transcription	Fetal Heart	heart
17	chr11:86886400-86896600	Weak transcription	Adipose Nuclei	Adipose
18	chr11:86886600-86891000	Weak transcription	HSMMtube	muscle
19	chr11:86886600-86891600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr11:86886800-86890400	Weak transcription	HepG2	liver
21	chr11:86887400-86891800	Weak transcription	Ovary	ovary
22	chr11:86887400-86899600	Weak transcription	NHDF-Ad	bronchial
23	chr11:86887600-86890200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr11:86887600-86893800	Weak transcription	NHLF	lung
25	chr11:86887600-86909400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr11:86888000-86891400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr11:86888800-86891600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr11:86889000-86891600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:86889200-86890400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr11:86889200-86891800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr11:86889400-86890200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr11:86889400-86899600	Weak transcription	Primary T cells from cord blood	blood
33	chr11:86889600-86891800	Weak transcription	A549	lung
34	chr11:86889600-86899200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr11:86889800-86890800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:86889800-86891400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr11:86889800-86893000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr11:86889800-86893000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr11:86889800-86893400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr11:86889800-86897400	Weak transcription	Fetal Intestine Small	intestine
41	chr11:86889800-86897800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr11:86889800-86898400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr11:86889800-86905200	Weak transcription	Fetal Lung	lung

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