Variant report

Variant	rs501505
Chromosome Location	chr11:85667916-85667917
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85667385..85669664-chr11:85671741..85675439,4	K562	blood:
2	chr11:85565045..85566988-chr11:85667216..85668779,2	MCF-7	breast:
3	chr11:85664911..85667444-chr11:85667862..85673209,4	K562	blood:
4	chr11:85667493..85669931-chr11:85675862..85677514,2	K562	blood:
5	chr11:85667904..85670774-chr11:85681620..85685057,3	K562	blood:
6	chr11:85666636..85668318-chr11:85679580..85681580,2	K562	blood:

Variant related genes	Relation type
ENSG00000150676	Chromatin interaction
ENSG00000215504	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1214669	0.81[EUR][1000 genomes]
rs12808312	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1949221	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2508381	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2508690	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2508692	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2508693	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2508696	0.90[ASN][1000 genomes]
rs2508697	0.82[EUR][1000 genomes]
rs3016240	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3016786	0.82[EUR][1000 genomes]
rs475639	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs484154	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs519778	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs529904	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs532470	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs541674	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs545592	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs553141	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs561646	0.85[ASN][1000 genomes]
rs563773	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs565031	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs572979	0.81[EUR][1000 genomes]
rs579406	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs587038	0.91[ASN][1000 genomes]
rs602222	0.90[ASN][1000 genomes]
rs604767	0.85[EUR][1000 genomes]
rs606505	0.91[ASN][1000 genomes]
rs609903	0.87[ASN][1000 genomes]
rs612396	0.81[ASN][1000 genomes]
rs613222	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs636355	0.87[ASN][1000 genomes]
rs636772	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs639012	0.88[ASN][1000 genomes]
rs642949	0.85[ASN][1000 genomes]
rs645299	0.90[ASN][1000 genomes]
rs647422	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs659863	0.81[ASN][1000 genomes]
rs664050	0.81[AFR][1000 genomes]
rs666682	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs671686	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs673751	0.95[ASN][1000 genomes]
rs676733	0.87[ASN][1000 genomes]
rs677869	0.81[ASN][1000 genomes]
rs677909	0.81[ASN][1000 genomes]
rs682928	0.82[ASN][1000 genomes]
rs683494	0.84[AMR][1000 genomes];0.89[EUR][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
rs501505	PICALM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85652800-85668800	Weak transcription	Small Intestine	intestine
2	chr11:85656000-85679800	Weak transcription	Fetal Brain Male	brain
3	chr11:85658600-85673000	Weak transcription	Right Ventricle	heart
4	chr11:85659400-85745800	Weak transcription	Stomach Mucosa	stomach
5	chr11:85660200-85670800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr11:85663400-85692000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:85663800-85740200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr11:85664200-85668200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr11:85664200-85673000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:85664400-85668000	Enhancers	Ovary	ovary
11	chr11:85664400-85668200	Strong transcription	Fetal Intestine Large	intestine
12	chr11:85664400-85673000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:85664400-85678600	Strong transcription	Adipose Nuclei	Adipose
14	chr11:85664400-85687200	Strong transcription	Primary T cells from cord blood	blood
15	chr11:85664400-85693600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr11:85664400-85699800	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr11:85664400-85726800	Strong transcription	Liver	Liver
18	chr11:85664400-85729000	Strong transcription	Placenta	Placenta
19	chr11:85664600-85668000	Strong transcription	Fetal Stomach	stomach
20	chr11:85664600-85668000	Strong transcription	Thymus	Thymus
21	chr11:85664600-85673000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:85664600-85693200	Strong transcription	Fetal Thymus	thymus
23	chr11:85664600-85730800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:85664800-85674200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:85664800-85678600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr11:85664800-85689400	Strong transcription	Primary B cells from cord blood	blood
27	chr11:85664800-85733000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr11:85665000-85668000	Genic enhancers	Fetal Muscle Leg	muscle
29	chr11:85665000-85671000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr11:85665000-85673600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:85665000-85679200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr11:85665200-85668000	Strong transcription	Fetal Brain Female	brain
33	chr11:85665200-85668400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr11:85665200-85668800	Weak transcription	Fetal Kidney	kidney
35	chr11:85665200-85669600	Weak transcription	Colonic Mucosa	Colon
36	chr11:85665200-85742600	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr11:85665200-85743000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr11:85665400-85678800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr11:85665400-85699800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr11:85665600-85679600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:85665600-85687800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr11:85665800-85668600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr11:85665800-85671800	Strong transcription	GM12878-XiMat	blood
44	chr11:85665800-85679600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr11:85665800-85699600	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr11:85665800-85701200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr11:85665800-85711400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:85666000-85668000	Enhancers	Fetal Heart	heart
49	chr11:85666000-85669000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr11:85666000-85669000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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