Variant report

Variant	rs597446
Chromosome Location	chr11:85775059-85775060
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

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	chr11:85775018..85777414-chr11:85781077..85783520,2	K562	blood:
4	chr11:85768733..85771194-chr11:85773077..85775713,3	MCF-7	breast:
5	chr11:85755134..85758081-chr11:85773891..85777241,3	K562	blood:
6	chr11:85773252..85777138-chr11:85860597..85863727,3	K562	blood:
7	chr11:85774766..85777240-chr11:85903999..85905671,2	K562	blood:
8	chr11:85775017..85777690-chr11:85953768..85955485,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000073921	Chromatin interaction
ENSG00000254699	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11234513	0.80[YRI][hapmap]
rs1513390	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1996108	0.87[ASN][1000 genomes]
rs2077815	0.80[ASN][1000 genomes]
rs2155051	0.91[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2458493	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2458496	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2458500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2508688	0.84[ASN][1000 genomes]
rs2509608	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2509609	0.90[ASN][1000 genomes]
rs3016786	0.80[CHB][hapmap]
rs475639	0.91[LWK][hapmap];0.95[MKK][hapmap];0.88[YRI][hapmap]
rs488134	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs489486	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs494369	0.82[ASN][1000 genomes]
rs497711	0.97[ASN][1000 genomes]
rs527162	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs528109	0.84[ASN][1000 genomes]
rs540422	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs542167	0.84[ASN][1000 genomes]
rs544458	0.96[ASN][1000 genomes]
rs544848	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs547767	0.86[ASN][1000 genomes]
rs564658	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs583126	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs585820	0.80[ASN][1000 genomes]
rs588076	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs588380	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]
rs592297	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs595972	0.80[ASN][1000 genomes]
rs596864	0.84[EUR][1000 genomes]
rs600258	0.82[ASN][1000 genomes]
rs600743	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs601185	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs602222	0.82[CHB][hapmap]
rs603615	0.82[ASN][1000 genomes]
rs604767	0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs613222	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs617836	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs618001	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs618629	0.83[ASN][1000 genomes]
rs622220	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs627818	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs629343	0.86[LWK][hapmap];0.81[MKK][hapmap]
rs634719	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs635168	0.95[ASN][1000 genomes]
rs637304	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs645299	0.84[CHB][hapmap]
rs648270	0.84[ASN][1000 genomes]
rs654194	0.80[ASN][1000 genomes]
rs655641	0.86[ASN][1000 genomes]
rs659023	0.84[LWK][hapmap]
rs664050	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs666682	0.88[ASW][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];0.88[YRI][hapmap]
rs669556	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs670606	0.80[ASN][1000 genomes]
rs680119	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs682366	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs682928	0.81[CHB][hapmap]
rs683340	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7938033	0.82[CHB][hapmap]
rs7951988	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9804630	1.00[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
rs597446	PICALM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 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	chr11:85764200-85775200	Weak transcription	Fetal Intestine Small	intestine
5	chr11:85764400-85777000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr11:85765600-85775400	Weak transcription	Placenta	Placenta
7	chr11:85765600-85777800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr11:85765800-85775200	Weak transcription	Brain Germinal Matrix	brain
9	chr11:85766000-85775400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:85768800-85776600	Enhancers	Liver	Liver
11	chr11:85769400-85776400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr11:85769400-85777200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr11:85770400-85776600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:85770600-85775200	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr11:85770800-85776600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr11:85770800-85776600	Weak transcription	Stomach Mucosa	stomach
17	chr11:85770800-85776800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr11:85770800-85777600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr11:85770800-85778200	Weak transcription	Gastric	stomach
20	chr11:85771000-85775400	Weak transcription	Small Intestine	intestine
21	chr11:85771200-85776600	Enhancers	HepG2	liver
22	chr11:85771800-85775400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:85771800-85775400	Weak transcription	Ovary	ovary
24	chr11:85772000-85775200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr11:85772200-85775600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr11:85772200-85777400	Weak transcription	Colonic Mucosa	Colon
27	chr11:85772400-85775400	Weak transcription	Fetal Muscle Leg	muscle
28	chr11:85772400-85775400	Weak transcription	Fetal Thymus	thymus
29	chr11:85772400-85775400	Active TSS	Right Atrium	heart
30	chr11:85772400-85776600	Weak transcription	Aorta	Aorta
31	chr11:85772600-85776600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:85772800-85775200	Enhancers	Rectal Smooth Muscle	rectum
33	chr11:85772800-85775400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr11:85772800-85775400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:85772800-85776600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:85772800-85777200	Enhancers	Primary B cells from peripheral blood	blood
37	chr11:85773000-85775600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:85773200-85775200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr11:85773200-85775400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr11:85773200-85776000	Enhancers	Brain Anterior Caudate	brain
41	chr11:85773200-85776600	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr11:85773200-85776600	Active TSS	K562	blood
43	chr11:85773200-85778200	Weak transcription	Pancreas	Pancrea
44	chr11:85773400-85777600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr11:85773600-85775400	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr11:85773600-85775400	Weak transcription	Left Ventricle	heart
47	chr11:85773600-85775400	Weak transcription	Lung	lung
48	chr11:85773600-85775400	Weak transcription	Psoas Muscle	Psoas
49	chr11:85773600-85775400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr11:85773600-85775600	Enhancers	Fetal Lung	lung

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