Variant report

Variant	rs3016786
Chromosome Location	chr11:85774562-85774563
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85774012..85776185-chr11:85778129..85779860,2	MCF-7	breast:
2	chr11:85773042..85775318-chr11:85782824..85785081,2	MCF-7	breast:
3	chr11:85768733..85771194-chr11:85773077..85775713,3	MCF-7	breast:
4	chr11:85755134..85758081-chr11:85773891..85777241,3	K562	blood:
5	chr11:85773252..85777138-chr11:85860597..85863727,3	K562	blood:

Variant related genes	Relation type
ENSG00000073921	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10751134	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs10792830	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10792831	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10792832	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10898438	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10898439	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1214669	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12808312	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1898895	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1949221	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1973630	0.87[ASN][1000 genomes]
rs2458500	0.81[CHB][hapmap]
rs2508381	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2508690	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2508691	0.92[ASN][1000 genomes]
rs2508692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2508693	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2508696	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2508697	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3016240	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851178	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3851179	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs475639	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs478711	0.85[ASN][1000 genomes]
rs484154	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs489486	0.81[CHB][hapmap]
rs493254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4944560	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs497816	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs501505	0.82[EUR][1000 genomes]
rs519778	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs526904	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs529904	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs532470	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs541674	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs542126	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs545592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs553141	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs561646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs563773	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs565031	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs572979	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs587038	0.85[ASN][1000 genomes]
rs597446	0.80[CHB][hapmap]
rs602222	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs604767	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs606505	0.85[ASN][1000 genomes]
rs609903	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs613222	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618001	0.80[CHB][hapmap]
rs629343	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs634719	0.81[CHB][hapmap]
rs636355	0.89[ASN][1000 genomes]
rs636772	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs638509	0.80[CEU][hapmap]
rs639012	0.80[ASN][1000 genomes]
rs642949	0.87[ASN][1000 genomes]
rs645299	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs647422	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs659023	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs659863	0.95[ASN][1000 genomes]
rs666682	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs669556	0.80[CHB][hapmap]
rs669813	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs671686	0.81[ASN][1000 genomes]
rs673751	0.81[ASN][1000 genomes]
rs676733	0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs677869	0.95[ASN][1000 genomes]
rs677909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs682928	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs683494	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs694011	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7114331	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7114401	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7129687	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs7941541	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7951988	0.83[CHB][hapmap]
rs867611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	nsv1050948	chr11:85756325-85968665	Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	nsv541117	chr11:85756325-85968665	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3016786	PICALM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85752800-85776400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr11:85756000-85776000	Weak transcription	Esophagus	oesophagus
3	chr11:85756600-85775400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:85764000-85775000	Weak transcription	Fetal Brain Female	brain
5	chr11:85764200-85774800	Weak transcription	HMEC	breast
6	chr11:85764200-85775200	Weak transcription	Fetal Intestine Small	intestine
7	chr11:85764400-85777000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr11:85765600-85775400	Weak transcription	Placenta	Placenta
9	chr11:85765600-85777800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr11:85765800-85775200	Weak transcription	Brain Germinal Matrix	brain
11	chr11:85766000-85775400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:85768800-85776600	Enhancers	Liver	Liver
13	chr11:85769400-85776400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr11:85769400-85777200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr11:85770400-85776600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:85770600-85775200	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr11:85770800-85776600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr11:85770800-85776600	Weak transcription	Stomach Mucosa	stomach
19	chr11:85770800-85776800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr11:85770800-85777600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr11:85770800-85778200	Weak transcription	Gastric	stomach
22	chr11:85771000-85775400	Weak transcription	Small Intestine	intestine
23	chr11:85771200-85776600	Enhancers	HepG2	liver
24	chr11:85771600-85775000	Enhancers	Osteobl	bone
25	chr11:85771800-85775000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr11:85771800-85775400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr11:85771800-85775400	Weak transcription	Ovary	ovary
28	chr11:85772000-85775000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr11:85772000-85775200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr11:85772200-85775600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr11:85772200-85777400	Weak transcription	Colonic Mucosa	Colon
32	chr11:85772400-85775400	Weak transcription	Fetal Muscle Leg	muscle
33	chr11:85772400-85775400	Weak transcription	Fetal Thymus	thymus
34	chr11:85772400-85775400	Active TSS	Right Atrium	heart
35	chr11:85772400-85776600	Weak transcription	Aorta	Aorta
36	chr11:85772600-85774800	Enhancers	Adipose Nuclei	Adipose
37	chr11:85772600-85776600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:85772800-85774800	Enhancers	NHLF	lung
39	chr11:85772800-85775200	Enhancers	Rectal Smooth Muscle	rectum
40	chr11:85772800-85775400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr11:85772800-85775400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr11:85772800-85776600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:85772800-85777200	Enhancers	Primary B cells from peripheral blood	blood
44	chr11:85773000-85774600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:85773000-85775600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:85773200-85775200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr11:85773200-85775400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr11:85773200-85776000	Enhancers	Brain Anterior Caudate	brain
49	chr11:85773200-85776600	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr11:85773200-85776600	Active TSS	K562	blood

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