Variant report

Variant	rs579406
Chromosome Location	chr11:85657759-85657760
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85653080..85655355-chr11:85655495..85657960,2	K562	blood:
2	chr11:85656909..85659832-chr11:85660162..85661872,3	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10792830	0.81[JPT][hapmap]
rs10792831	0.81[JPT][hapmap]
rs12808312	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1898895	0.82[JPT][hapmap]
rs1949221	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2508381	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2508690	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2508692	0.93[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs2508693	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2508696	0.82[JPT][hapmap]
rs3016240	0.82[EUR][1000 genomes]
rs3016786	0.92[CEU][hapmap]
rs475639	1.00[CEU][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs484154	0.92[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs493254	0.85[JPT][hapmap]
rs4944560	0.81[JPT][hapmap]
rs497816	0.86[JPT][hapmap]
rs501505	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs526904	0.82[JPT][hapmap]
rs529904	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs532470	0.92[CEU][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs541674	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs542126	0.82[JPT][hapmap]
rs545592	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs553141	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs561646	0.82[JPT][hapmap]
rs563773	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs565031	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs597446	0.83[YRI][hapmap]
rs602222	0.81[JPT][hapmap]
rs604767	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs609903	0.81[JPT][hapmap]
rs612396	0.80[AMR][1000 genomes]
rs613222	0.96[CEU][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs618001	0.83[YRI][hapmap]
rs629343	0.81[JPT][hapmap]
rs636772	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs647422	0.80[EUR][1000 genomes]
rs666682	0.96[CEU][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs669813	0.81[JPT][hapmap]
rs671686	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs677909	0.81[JPT][hapmap]
rs682928	0.81[JPT][hapmap]
rs683340	0.93[AFR][1000 genomes]
rs683494	0.96[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs694011	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs7114331	0.81[JPT][hapmap]
rs7114401	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	nsv1053599	chr11:85641619-85684353	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv1040567	chr11:85641619-85684935	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs579406	PICALM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85646600-85660000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:85646600-85667400	Weak transcription	Gastric	stomach
3	chr11:85652800-85664400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr11:85652800-85668800	Weak transcription	Small Intestine	intestine
5	chr11:85653000-85657800	Weak transcription	Ovary	ovary
6	chr11:85653000-85658200	Weak transcription	Left Ventricle	heart
7	chr11:85653000-85658400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr11:85654200-85658400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr11:85656000-85661000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:85656000-85679800	Weak transcription	Fetal Brain Male	brain
11	chr11:85656200-85658600	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr11:85656200-85661000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr11:85656400-85658600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:85656400-85660200	Enhancers	Adipose Nuclei	Adipose
15	chr11:85656400-85660200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr11:85656400-85660200	Enhancers	HUVEC	blood vessel
17	chr11:85656600-85658400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:85656600-85659400	Enhancers	Right Atrium	heart
19	chr11:85656600-85662400	Enhancers	HepG2	liver
20	chr11:85656800-85658200	Enhancers	Brain Substantia Nigra	brain
21	chr11:85656800-85659000	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr11:85656800-85659600	Enhancers	Brain Cingulate Gyrus	brain
23	chr11:85656800-85660200	Enhancers	Brain Hippocampus Middle	brain
24	chr11:85656800-85661400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:85657000-85659000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr11:85657000-85659000	Enhancers	Brain Anterior Caudate	brain
27	chr11:85657000-85659400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr11:85657000-85659600	Enhancers	Brain Angular Gyrus	brain
29	chr11:85657000-85660200	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr11:85657000-85660600	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr11:85657000-85661000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:85657200-85657800	Weak transcription	HMEC	breast
33	chr11:85657200-85658000	Weak transcription	Liver	Liver
34	chr11:85657200-85659400	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr11:85657200-85660000	Weak transcription	Placenta	Placenta
36	chr11:85657200-85665600	Weak transcription	Lung	lung
37	chr11:85657400-85658600	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr11:85657400-85658800	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr11:85657400-85659400	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr11:85657400-85660400	Enhancers	NHDF-Ad	bronchial
41	chr11:85657400-85660800	Enhancers	Osteobl	bone
42	chr11:85657600-85657800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr11:85657600-85658400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:85657600-85658600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr11:85657600-85660400	Enhancers	NHEK	skin
46	chr11:85657600-85665600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:85657600-85666600	Weak transcription	Spleen	Spleen

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