Variant report

Variant	rs647422
Chromosome Location	chr11:85759746-85759747
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85758317..85760052-chr11:85763851..85765392,2	MCF-7	breast:
2	chr11:85756990..85760040-chr11:85954686..85957890,3	K562	blood:
3	chr11:85758079..85763459-chr11:85776941..85781307,6	MCF-7	breast:
4	chr11:85759040..85760560-chr11:85914409..85916146,2	K562	blood:
5	chr11:85759414..85762040-chr11:85764190..85765879,2	K562	blood:
6	chr11:85759677..85764331-chr11:85767246..85771680,6	K562	blood:

Variant related genes	Relation type
ENSG00000074266	Chromatin interaction
ENSG00000073921	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1214669	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12808312	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1949221	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1973630	0.90[ASN][1000 genomes]
rs2508381	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2508690	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2508691	0.94[ASN][1000 genomes]
rs2508692	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2508693	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2508696	0.89[ASN][1000 genomes]
rs2508697	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3016240	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3016786	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs475639	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs478711	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs484154	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs493254	0.94[ASN][1000 genomes]
rs501505	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs519778	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529904	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs532470	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs541674	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs545592	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs553141	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs561646	0.94[ASN][1000 genomes]
rs563773	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs565031	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs572979	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs579406	0.80[EUR][1000 genomes]
rs587038	0.87[ASN][1000 genomes]
rs602222	0.89[ASN][1000 genomes]
rs604767	0.89[EUR][1000 genomes]
rs606505	0.87[ASN][1000 genomes]
rs609903	0.92[ASN][1000 genomes]
rs613222	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs636355	0.92[ASN][1000 genomes]
rs636772	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs639012	0.83[ASN][1000 genomes]
rs642949	0.89[ASN][1000 genomes]
rs645299	0.89[ASN][1000 genomes]
rs659863	0.98[ASN][1000 genomes]
rs666682	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs669813	0.94[ASN][1000 genomes]
rs671686	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs673751	0.83[ASN][1000 genomes]
rs676733	0.92[ASN][1000 genomes]
rs677869	0.98[ASN][1000 genomes]
rs677909	0.98[ASN][1000 genomes]
rs682928	0.88[ASN][1000 genomes]
rs683494	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs694011	0.99[ASN][1000 genomes]
rs867611	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	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
6	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
7	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
rs647422	PICALM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85746600-85762800	Weak transcription	Stomach Mucosa	stomach
2	chr11:85751400-85761800	Enhancers	Liver	Liver
3	chr11:85751800-85760600	Enhancers	Primary T cells from cord blood	blood
4	chr11:85751800-85761200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr11:85752400-85760600	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr11:85752400-85768400	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr11:85752800-85768200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr11:85752800-85776400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:85753000-85763000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr11:85753200-85762200	Enhancers	Adipose Nuclei	Adipose
11	chr11:85753200-85764600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:85753200-85768000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr11:85754000-85764000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr11:85754200-85764000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr11:85754200-85765200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr11:85754400-85759800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr11:85754400-85763000	Weak transcription	HUVEC	blood vessel
18	chr11:85754400-85768200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr11:85754600-85762600	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr11:85755200-85761200	Enhancers	Primary T cells fromperipheralblood	blood
21	chr11:85755200-85762800	Weak transcription	Fetal Lung	lung
22	chr11:85755600-85761400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr11:85755800-85760600	Enhancers	Brain Substantia Nigra	brain
24	chr11:85755800-85763000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:85755800-85764000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr11:85755800-85764000	Weak transcription	HepG2	liver
27	chr11:85756000-85760200	Weak transcription	Placenta	Placenta
28	chr11:85756000-85761800	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr11:85756000-85763800	Weak transcription	Spleen	Spleen
30	chr11:85756000-85764200	Weak transcription	Aorta	Aorta
31	chr11:85756000-85765400	Weak transcription	Fetal Muscle Leg	muscle
32	chr11:85756000-85767000	Enhancers	Brain Hippocampus Middle	brain
33	chr11:85756000-85776000	Weak transcription	Esophagus	oesophagus
34	chr11:85756600-85760400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr11:85756600-85763800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr11:85756600-85763800	Weak transcription	Gastric	stomach
37	chr11:85756600-85765400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr11:85756600-85775400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:85756800-85759800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr11:85756800-85760000	Enhancers	Fetal Heart	heart
41	chr11:85756800-85760200	Enhancers	Colon Smooth Muscle	Colon
42	chr11:85756800-85761000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr11:85757000-85760200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:85757200-85759800	Enhancers	Small Intestine	intestine
45	chr11:85757400-85762200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr11:85757600-85761800	Enhancers	Primary B cells from cord blood	blood
47	chr11:85757600-85762400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr11:85757800-85760800	Enhancers	Psoas Muscle	Psoas
49	chr11:85758200-85760800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:85758200-85765600	Enhancers	Ovary	ovary

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