Variant report

Variant	rs3016240
Chromosome Location	chr11:85750812-85750813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85741019..85743980-chr11:85750116..85753197,4	K562	blood:
2	chr11:85750217..85751892-chr11:85925009..85927244,2	MCF-7	breast:
3	chr11:85750532..85752691-chr11:85830646..85833221,2	K562	blood:
4	chr11:85750753..85754921-chr11:85777860..85781815,4	MCF-7	breast:
5	chr11:85745012..85747754-chr11:85749922..85752779,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073921	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1214669	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12808312	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1949221	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1973630	0.90[ASN][1000 genomes]
rs2508381	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2508690	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2508691	0.94[ASN][1000 genomes]
rs2508692	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2508693	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2508696	0.90[ASN][1000 genomes]
rs2508697	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3016786	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs475639	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs478711	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs484154	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs493254	0.94[ASN][1000 genomes]
rs501505	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs519778	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs529904	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs532470	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs541674	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs545592	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs553141	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs561646	0.95[ASN][1000 genomes]
rs563773	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs565031	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs572979	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs579406	0.82[EUR][1000 genomes]
rs587038	0.89[ASN][1000 genomes]
rs602222	0.90[ASN][1000 genomes]
rs604767	0.85[EUR][1000 genomes]
rs606505	0.89[ASN][1000 genomes]
rs609903	0.93[ASN][1000 genomes]
rs612396	0.81[AMR][1000 genomes]
rs613222	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs636355	0.93[ASN][1000 genomes]
rs636772	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs639012	0.83[ASN][1000 genomes]
rs642949	0.91[ASN][1000 genomes]
rs645299	0.90[ASN][1000 genomes]
rs647422	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs659863	0.99[ASN][1000 genomes]
rs666682	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs669813	0.94[ASN][1000 genomes]
rs671686	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs673751	0.85[ASN][1000 genomes]
rs676733	0.93[ASN][1000 genomes]
rs677869	0.99[ASN][1000 genomes]
rs677909	0.99[ASN][1000 genomes]
rs682928	0.88[ASN][1000 genomes]
rs683494	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs694011	0.98[ASN][1000 genomes]
rs867611	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv468770	chr11:85688209-85751883	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv555642	chr11:85688209-85751883	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv468771	chr11:85688209-85757589	Strong transcription Enhancers Genic enhancers 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	9 gene(s)	inside rSNPs	diseases
9	nsv468773	chr11:85688209-85757589	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv555643	chr11:85688209-85757589	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv468774	chr11:85688209-85775059	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv555644	chr11:85688209-85775059	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv1829985	chr11:85740319-85789350	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3016240	PICALM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85731600-85754200	Weak transcription	Brain Germinal Matrix	brain
2	chr11:85733200-85754000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:85737000-85752800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:85737200-85751800	Weak transcription	NHLF	lung
5	chr11:85737200-85755200	Weak transcription	Lung	lung
6	chr11:85737200-85755600	Weak transcription	Esophagus	oesophagus
7	chr11:85738400-85752400	Weak transcription	Fetal Kidney	kidney
8	chr11:85738800-85752000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr11:85740400-85751800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr11:85740400-85755600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:85740600-85752600	Weak transcription	NHEK	skin
12	chr11:85740800-85754000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr11:85741400-85751800	Weak transcription	HMEC	breast
14	chr11:85742000-85752000	Weak transcription	NHDF-Ad	bronchial
15	chr11:85742000-85752200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr11:85742200-85751800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr11:85742200-85754000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr11:85742200-85755000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr11:85742200-85755400	Weak transcription	Aorta	Aorta
20	chr11:85742400-85751800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:85742400-85752000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr11:85742400-85752400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr11:85742400-85752400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr11:85742400-85752800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr11:85742600-85751800	Weak transcription	Fetal Lung	lung
26	chr11:85742600-85751800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr11:85742600-85752400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr11:85742600-85752800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr11:85742600-85752800	Weak transcription	Dnd41	blood
30	chr11:85742600-85753800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr11:85742600-85754000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr11:85742600-85755600	Weak transcription	Placenta	Placenta
33	chr11:85742800-85758400	Weak transcription	Fetal Intestine Large	intestine
34	chr11:85743000-85752600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:85744600-85752000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr11:85744800-85751800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr11:85744800-85752200	Weak transcription	Primary B cells from cord blood	blood
38	chr11:85744800-85753000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr11:85744800-85753800	Weak transcription	Ovary	ovary
40	chr11:85745600-85751400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr11:85745800-85751600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr11:85746000-85751200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr11:85746000-85751800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr11:85746200-85751600	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr11:85746200-85751600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:85746200-85751600	Weak transcription	Colon Smooth Muscle	Colon
47	chr11:85746200-85751800	Weak transcription	Primary T cells from cord blood	blood
48	chr11:85746200-85752400	Weak transcription	Hela-S3	cervix
49	chr11:85746200-85753200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr11:85746400-85751400	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links