Variant report

Variant	rs7952366
Chromosome Location	chr11:119597943-119597944
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF2	chr11:119597908-119598099	GM12878	blood:	n/a	n/a
2	MAX	chr11:119597768-119598634	H1-hESC	embryonic stem cell:	n/a	chr11:119598584-119598594 chr11:119598070-119598085 chr11:119598072-119598087 chr11:119598074-119598083 chr11:119598074-119598083 chr11:119598072-119598085 chr11:119598073-119598082 chr11:119598073-119598083 chr11:119598075-119598082 chr11:119598074-119598084 chr11:119598073-119598084 chr11:119598073-119598083 chr11:119598072-119598085 chr11:119598073-119598084 chr11:119598072-119598085
3	MAX	chr11:119597932-119598594	ECC-1	luminal epithelium:	n/a	chr11:119598584-119598594 chr11:119598070-119598085 chr11:119598072-119598087 chr11:119598074-119598083 chr11:119598074-119598083 chr11:119598072-119598085 chr11:119598073-119598082 chr11:119598073-119598083 chr11:119598075-119598082 chr11:119598074-119598084 chr11:119598073-119598084 chr11:119598073-119598083 chr11:119598072-119598085 chr11:119598073-119598084 chr11:119598072-119598085
4	USF1	chr11:119597898-119598233	H1-hESC	embryonic stem cell:	n/a	n/a
5	MTA3	chr11:119597812-119598468	GM12878	blood:	n/a	n/a
6	SIN3A	chr11:119597072-119600964	H1-hESC	embryonic stem cell:	n/a	chr11:119598510-119598523 chr11:119597118-119597129 chr11:119599794-119599805 chr11:119599846-119599857 chr11:119599845-119599858
7	USF1	chr11:119597848-119598236	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr11:119597886-119598196	K562	blood:	n/a	chr11:119598070-119598085 chr11:119598072-119598087 chr11:119598074-119598083 chr11:119598074-119598083 chr11:119598072-119598085 chr11:119598073-119598082 chr11:119598073-119598083 chr11:119598075-119598082 chr11:119598074-119598084 chr11:119598073-119598084 chr11:119598073-119598083 chr11:119598072-119598085 chr11:119598073-119598084 chr11:119598072-119598085
9	REST	chr11:119597919-119600693	H1-neurons	neurons:	n/a	chr11:119599848-119599861 chr11:119599304-119599317 chr11:119598617-119598630 chr11:119599848-119599861 chr11:119599845-119599858 chr11:119600480-119600493 chr11:119600483-119600496 chr11:119599290-119599303 chr11:119598510-119598523 chr11:119599302-119599320 chr11:119599040-119599053
10	MAZ	chr11:119597671-119601057	IMR90	lung:	n/a	chr11:119598584-119598594 chr11:119598070-119598085 chr11:119598072-119598087 chr11:119598074-119598083 chr11:119598074-119598083 chr11:119598072-119598085 chr11:119598073-119598082 chr11:119598073-119598083 chr11:119598075-119598082 chr11:119598074-119598084 chr11:119598073-119598084 chr11:119598073-119598083 chr11:119598072-119598085 chr11:119598073-119598084 chr11:119598072-119598085
11	MAX	chr11:119597942-119598209	H1-hESC	embryonic stem cell:	n/a	chr11:119598070-119598085 chr11:119598072-119598087 chr11:119598074-119598083 chr11:119598074-119598083 chr11:119598072-119598085 chr11:119598073-119598082 chr11:119598073-119598083 chr11:119598075-119598082 chr11:119598074-119598084 chr11:119598073-119598084 chr11:119598073-119598083 chr11:119598072-119598085 chr11:119598073-119598084 chr11:119598072-119598085
12	ELF1	chr11:119597940-119598836	GM12878	blood:	n/a	n/a
13	RAD21	chr11:119597368-119601907	SK-N-SH	brain:	n/a	chr11:119599960-119599970 chr11:119600188-119600207
14	MAX	chr11:119597788-119598434	H1-hESC	embryonic stem cell:	n/a	chr11:119598070-119598085 chr11:119598072-119598087 chr11:119598074-119598083 chr11:119598074-119598083 chr11:119598072-119598085 chr11:119598073-119598082 chr11:119598073-119598083 chr11:119598075-119598082 chr11:119598074-119598084 chr11:119598073-119598084 chr11:119598073-119598083 chr11:119598072-119598085 chr11:119598073-119598084 chr11:119598072-119598085
15	SMC3	chr11:119597227-119601922	SK-N-SH	brain:	n/a	chr11:119598367-119598374 chr11:119599984-119599994 chr11:119600192-119600206
16	USF1	chr11:119597876-119598209	SK-N-SH_RA	brain:	n/a	n/a
17	MAX	chr11:119597852-119598302	MCF-7	breast:	n/a	chr11:119598070-119598085 chr11:119598072-119598087 chr11:119598074-119598083 chr11:119598074-119598083 chr11:119598072-119598085 chr11:119598073-119598082 chr11:119598073-119598083 chr11:119598075-119598082 chr11:119598074-119598084 chr11:119598073-119598084 chr11:119598073-119598083 chr11:119598072-119598085 chr11:119598073-119598084 chr11:119598072-119598085
18	MXI1	chr11:119597064-119601983	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:119593045..119595193-chr11:119597284..119598893,2	K562	blood:
2	chr11:119596678..119598244-chr11:120080691..120083060,2	K562	blood:

Variant related genes	Relation type
ENSG00000254854	TF binding region
ENSG00000184232	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10790339	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10892444	0.84[CEU][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10892445	0.82[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10892446	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11217426	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11217429	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11217430	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11217434	0.81[AMR][1000 genomes]
rs11217437	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11217438	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11217440	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11217441	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11217442	0.91[EUR][1000 genomes]
rs11217448	0.90[EUR][1000 genomes]
rs11607610	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12361192	0.83[EUR][1000 genomes]
rs12418662	0.83[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12421434	0.81[CEU][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12421466	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12786505	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12793075	0.81[CEU][hapmap];0.85[MEX][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12796806	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12800445	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1876795	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2136420	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2136421	0.85[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2368936	0.81[CEU][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35248712	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3829260	0.81[EUR][1000 genomes]
rs4245206	0.81[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4489755	0.94[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4505073	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs4936496	0.81[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4938718	0.81[CEU][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4938719	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4938720	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58136657	0.91[EUR][1000 genomes]
rs6589770	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73006720	0.91[EUR][1000 genomes]
rs9666263	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898421	chr11:119499014-119631325	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv898422	chr11:119518006-119601779	Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv898423	chr11:119541332-119659753	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1051769	chr11:119572865-119630769	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1037739	chr11:119592989-119630641	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7952366	SORL1	cis	cerebellum	SCAN
rs7952366	DDX6	cis	cerebellum	SCAN
rs7952366	YARS2	trans	parietal	SCAN
rs7952366	HSPA8	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119595800-119598200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
2	chr11:119596000-119598000	Flanking Active TSS	Brain Cingulate Gyrus	brain
3	chr11:119596000-119598400	Flanking Active TSS	Brain Angular Gyrus	brain
4	chr11:119596400-119598200	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr11:119596400-119598400	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr11:119596600-119598000	Enhancers	Left Ventricle	heart
7	chr11:119596600-119598800	Flanking Active TSS	Brain Hippocampus Middle	brain
8	chr11:119596600-119600400	Active TSS	Esophagus	oesophagus
9	chr11:119596800-119598000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:119596800-119598000	Enhancers	Fetal Heart	heart
11	chr11:119596800-119598000	Bivalent Enhancer	Fetal Thymus	thymus
12	chr11:119596800-119598200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
13	chr11:119597000-119598000	Enhancers	Lung	lung
14	chr11:119597000-119598000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
15	chr11:119597000-119598200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:119597000-119598200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:119597000-119598200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
18	chr11:119597000-119598200	Enhancers	Spleen	Spleen
19	chr11:119597000-119598600	Flanking Active TSS	Fetal Brain Male	brain
20	chr11:119597000-119599200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr11:119597000-119599200	Flanking Active TSS	GM12878-XiMat	blood
22	chr11:119597200-119598000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
23	chr11:119597200-119598000	Weak transcription	Small Intestine	intestine
24	chr11:119597200-119598200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr11:119597200-119598200	Enhancers	Fetal Lung	lung
26	chr11:119597200-119598800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
27	chr11:119597200-119599200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr11:119597200-119599200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:119597200-119599200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
30	chr11:119597200-119599600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr11:119597200-119600400	Active TSS	H1 Cell Line	embryonic stem cell
32	chr11:119597200-119600400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:119597200-119600400	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr11:119597200-119600800	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr11:119597200-119601000	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr11:119597200-119601000	Active TSS	H9 Cell Line	embryonic stem cell
37	chr11:119597400-119598000	Enhancers	Colon Smooth Muscle	Colon
38	chr11:119597400-119598000	Flanking Active TSS	Fetal Intestine Small	intestine
39	chr11:119597400-119598200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
40	chr11:119597400-119598200	Enhancers	Liver	Liver
41	chr11:119597400-119598200	Flanking Active TSS	Pancreas	Pancrea
42	chr11:119597400-119598400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr11:119597400-119598400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr11:119597400-119598400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
45	chr11:119597400-119598800	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr11:119597400-119599200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr11:119597400-119600600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr11:119597400-119600800	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr11:119597400-119601000	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr11:119597400-119601000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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