Variant report

Variant	rs671686
Chromosome Location	chr11:85681479-85681480
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85660136..85662159-chr11:85679695..85681891,2	K562	blood:
2	chr11:85666636..85668318-chr11:85679580..85681580,2	K562	blood:

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10751134	0.95[JPT][hapmap]
rs10792830	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10792831	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10792832	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs10898438	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10898439	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12808312	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1898895	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1949221	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1973630	0.83[ASN][1000 genomes]
rs2508381	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2508690	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2508691	0.87[ASN][1000 genomes]
rs2508692	0.93[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2508693	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2508696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3016240	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3016786	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3851178	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs3851179	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs475639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs484154	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs493254	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4944560	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs497816	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs501505	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs519778	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs526904	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs529904	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs532470	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs541674	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs542126	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs545592	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs553141	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs561646	0.96[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs563773	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs565031	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs579406	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs587038	0.93[ASN][1000 genomes]
rs601185	0.80[CHB][hapmap]
rs602222	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs604767	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs606505	0.93[ASN][1000 genomes]
rs609903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs613222	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs629343	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs636355	0.89[ASN][1000 genomes]
rs636772	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs639012	0.99[ASN][1000 genomes]
rs642949	0.87[ASN][1000 genomes]
rs645299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs647422	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs659023	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs659863	0.83[ASN][1000 genomes]
rs666682	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs669813	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs673751	0.92[ASN][1000 genomes]
rs676733	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs677869	0.83[ASN][1000 genomes]
rs677909	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs682928	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs683494	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs694011	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7114331	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7114401	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7129687	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs7941541	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7951988	0.86[CHB][hapmap]
rs867611	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

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
rs671686	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	chr11:85668000-85681600	Weak transcription	Fetal Brain Female	brain
25	chr11:85668000-85691400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr11:85669400-85686200	Strong transcription	Fetal Intestine Large	intestine
27	chr11:85670000-85715800	Weak transcription	Colonic Mucosa	Colon
28	chr11:85671800-85710600	Weak transcription	Psoas Muscle	Psoas
29	chr11:85672400-85685400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:85673200-85702800	Weak transcription	Small Intestine	intestine
31	chr11:85673400-85681600	Weak transcription	Esophagus	oesophagus
32	chr11:85673800-85681600	Weak transcription	Gastric	stomach
33	chr11:85674000-85685000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr11:85674000-85695200	Strong transcription	HSMM	muscle
35	chr11:85674000-85708600	Strong transcription	K562	blood
36	chr11:85674200-85715400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr11:85675000-85693200	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr11:85675000-85742600	Strong transcription	Primary B cells from peripheral blood	blood
39	chr11:85675200-85700000	Strong transcription	GM12878-XiMat	blood
40	chr11:85675400-85683800	Strong transcription	HMEC	breast
41	chr11:85675400-85693200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr11:85675600-85693000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:85676200-85684600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr11:85676800-85681800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr11:85676800-85684400	Weak transcription	Brain Germinal Matrix	brain
46	chr11:85677400-85682200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr11:85677600-85682400	Weak transcription	Right Ventricle	heart
48	chr11:85677800-85709600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr11:85678000-85681600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr11:85678000-85681600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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