Variant report

Variant	rs588380
Chromosome Location	chr11:85684935-85684936
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85683941..85685455-chr11:85694454..85696370,2	K562	blood:
2	chr11:85667904..85670774-chr11:85681620..85685057,3	K562	blood:

Variant related genes	Relation type
ENSG00000073921	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1513390	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1996108	0.94[ASN][1000 genomes]
rs2077815	0.95[ASN][1000 genomes]
rs2155051	0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs2458493	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2458496	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2458499	0.87[ASN][1000 genomes]
rs2458500	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2508688	0.97[ASN][1000 genomes]
rs2509608	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs472618	0.92[ASN][1000 genomes]
rs488134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs489486	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs494369	0.90[ASN][1000 genomes]
rs497711	0.84[ASN][1000 genomes]
rs504129	0.89[ASN][1000 genomes]
rs527162	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs528109	0.98[ASN][1000 genomes]
rs540422	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs542167	0.97[ASN][1000 genomes]
rs544848	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs547767	0.87[ASN][1000 genomes]
rs548121	0.90[ASN][1000 genomes]
rs564658	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs583126	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs585820	0.93[ASN][1000 genomes]
rs588076	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs592297	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs592314	0.90[ASN][1000 genomes]
rs595972	0.93[ASN][1000 genomes]
rs596864	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs597446	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs600258	0.95[ASN][1000 genomes]
rs600743	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs601185	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs602222	0.85[CHB][hapmap]
rs602391	0.88[ASN][1000 genomes]
rs603615	0.96[ASN][1000 genomes]
rs616555	0.91[ASN][1000 genomes]
rs617836	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs618001	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs618629	0.98[ASN][1000 genomes]
rs618679	0.89[ASN][1000 genomes]
rs622220	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs626542	0.93[ASN][1000 genomes]
rs627818	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs634719	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs637304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs645299	0.89[CHB][hapmap]
rs648270	0.89[ASN][1000 genomes]
rs654194	0.93[ASN][1000 genomes]
rs655641	0.94[ASN][1000 genomes]
rs659801	0.82[ASN][1000 genomes]
rs664050	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs669556	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs670606	0.93[ASN][1000 genomes]
rs680119	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs682366	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs682928	0.85[CHB][hapmap]
rs683340	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs683494	0.88[YRI][hapmap]
rs7938033	0.90[CHB][hapmap];0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs7951988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9804630	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
8	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
9	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
10	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs588380	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	chr11:85663400-85692000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:85663800-85740200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:85664400-85687200	Strong transcription	Primary T cells from cord blood	blood
5	chr11:85664400-85693600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr11:85664400-85699800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr11:85664400-85726800	Strong transcription	Liver	Liver
8	chr11:85664400-85729000	Strong transcription	Placenta	Placenta
9	chr11:85664600-85693200	Strong transcription	Fetal Thymus	thymus
10	chr11:85664600-85730800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:85664800-85689400	Strong transcription	Primary B cells from cord blood	blood
12	chr11:85664800-85733000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr11:85665200-85742600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr11:85665200-85743000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:85665400-85699800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr11:85665600-85687800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr11:85665800-85699600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr11:85665800-85701200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr11:85665800-85711400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:85666000-85735800	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr11:85666400-85693600	Strong transcription	Primary hematopoietic stem cells	blood
22	chr11:85667800-85701800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:85667800-85712000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr11:85668000-85691400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr11:85669400-85686200	Strong transcription	Fetal Intestine Large	intestine
26	chr11:85670000-85715800	Weak transcription	Colonic Mucosa	Colon
27	chr11:85671800-85710600	Weak transcription	Psoas Muscle	Psoas
28	chr11:85672400-85685400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:85673200-85702800	Weak transcription	Small Intestine	intestine
30	chr11:85674000-85685000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr11:85674000-85695200	Strong transcription	HSMM	muscle
32	chr11:85674000-85708600	Strong transcription	K562	blood
33	chr11:85674200-85715400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr11:85675000-85693200	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr11:85675000-85742600	Strong transcription	Primary B cells from peripheral blood	blood
36	chr11:85675200-85700000	Strong transcription	GM12878-XiMat	blood
37	chr11:85675400-85693200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:85675600-85693000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:85677800-85709600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:85678000-85690200	Weak transcription	Pancreas	Pancrea
41	chr11:85679200-85685600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:85679400-85688600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr11:85679600-85687600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr11:85679800-85697000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr11:85680000-85693600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr11:85680400-85685000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr11:85680400-85685400	Weak transcription	Fetal Brain Male	brain
48	chr11:85680600-85685000	Strong transcription	Fetal Lung	lung
49	chr11:85680600-85685200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr11:85680600-85685200	Strong transcription	Muscle Satellite Cultured Cells	--

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