Variant report

Variant	rs613222
Chromosome Location	chr11:85769105-85769106
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85768733..85771194-chr11:85773077..85775713,3	MCF-7	breast:
2	chr11:85768233..85770657-chr11:85911985..85913899,2	K562	blood:
3	chr11:85768255..85771189-chr11:85904324..85906270,2	K562	blood:
4	chr11:85767944..85769577-chr11:85771277..85773759,2	MCF-7	breast:
5	chr11:85763399..85766390-chr11:85766683..85769520,2	K562	blood:
6	chr11:85759677..85764331-chr11:85767246..85771680,6	K562	blood:

Variant related genes	Relation type
ENSG00000254502	Chromatin interaction
ENSG00000254699	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10751134	0.95[JPT][hapmap]
rs10792830	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10792831	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10792832	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10898438	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10898439	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs1214669	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12808312	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1513390	0.89[AFR][1000 genomes]
rs1898895	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1949221	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1973630	0.87[ASN][1000 genomes]
rs2508381	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2508690	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2508691	0.92[ASN][1000 genomes]
rs2508692	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2508693	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2508696	0.96[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2508697	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3016240	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3016786	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]
rs3851178	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3851179	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs475639	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs478711	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs484154	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs493254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4944560	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs497816	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs501505	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs519778	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs526904	0.96[CHB][hapmap];1.00[JPT][hapmap]
rs529904	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs532470	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs541674	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs542126	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs545592	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs553141	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs561646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs563773	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs565031	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs572979	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs579406	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs583126	0.90[AFR][1000 genomes]
rs587038	0.85[ASN][1000 genomes]
rs597446	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs602222	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs604767	0.93[CEU][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs606505	0.85[ASN][1000 genomes]
rs609903	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs618001	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs629343	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs636355	0.89[ASN][1000 genomes]
rs636772	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs639012	0.80[ASN][1000 genomes]
rs642949	0.87[ASN][1000 genomes]
rs645299	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs647422	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs659023	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs659863	0.95[ASN][1000 genomes]
rs666682	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs669813	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs671686	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs673751	0.81[ASN][1000 genomes]
rs676733	0.95[CHB][hapmap];0.95[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	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs683494	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs694011	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7114331	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs7114401	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs7129687	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7941541	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs7951988	0.81[CHB][hapmap]
rs867611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[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
rs613222	PICALM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 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	chr11:85758600-85774400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr11:85759000-85773600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr11:85759400-85773800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr11:85759400-85774400	Weak transcription	NHEK	skin
8	chr11:85759800-85772600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:85760200-85773000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:85760400-85772000	Weak transcription	Pancreas	Pancrea
11	chr11:85762200-85773800	Weak transcription	NHDF-Ad	bronchial
12	chr11:85762400-85773000	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr11:85763200-85772800	Weak transcription	NHLF	lung
14	chr11:85764000-85775000	Weak transcription	Fetal Brain Female	brain
15	chr11:85764200-85774800	Weak transcription	HMEC	breast
16	chr11:85764200-85775200	Weak transcription	Fetal Intestine Small	intestine
17	chr11:85764400-85769400	Weak transcription	Small Intestine	intestine
18	chr11:85764400-85770400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:85764400-85771600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr11:85764400-85772600	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr11:85764400-85777000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr11:85764600-85769400	Weak transcription	Stomach Mucosa	stomach
23	chr11:85764600-85770600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr11:85765000-85773000	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr11:85765000-85773200	Weak transcription	Lung	lung
26	chr11:85765400-85769400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr11:85765600-85770000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr11:85765600-85770400	Weak transcription	Gastric	stomach
29	chr11:85765600-85770600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr11:85765600-85770600	Weak transcription	Ovary	ovary
31	chr11:85765600-85771200	Weak transcription	HepG2	liver
32	chr11:85765600-85771200	Weak transcription	HUVEC	blood vessel
33	chr11:85765600-85772400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr11:85765600-85773200	Weak transcription	Spleen	Spleen
35	chr11:85765600-85773800	Weak transcription	Dnd41	blood
36	chr11:85765600-85775400	Weak transcription	Placenta	Placenta
37	chr11:85765600-85777800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr11:85765800-85769400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr11:85765800-85769400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr11:85765800-85769600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr11:85765800-85770400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr11:85765800-85770400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr11:85765800-85771200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr11:85765800-85775200	Weak transcription	Brain Germinal Matrix	brain
45	chr11:85766000-85769200	Weak transcription	Duodenum Mucosa	Duodenum
46	chr11:85766000-85769400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr11:85766000-85769800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr11:85766000-85770400	Weak transcription	Left Ventricle	heart
49	chr11:85766000-85770400	Weak transcription	Psoas Muscle	Psoas
50	chr11:85766000-85770400	Weak transcription	Right Atrium	heart

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