Variant report

Variant	rs1079452
Chromosome Location	chr11:8779172-8779173
allele	C/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	JUND	chr11:8778685-8779268	SK-N-SH	brain:	n/a	chr11:8778881-8778891 chr11:8778882-8778890 chr11:8778881-8778891 chr11:8778883-8778890 chr11:8778882-8778890 chr11:8778880-8778891 chr11:8778881-8778891 chr11:8778878-8778889 chr11:8778881-8778891
2	FOSL2	chr11:8778570-8779189	SK-N-SH	brain:	n/a	chr11:8778881-8778891 chr11:8778882-8778890 chr11:8778881-8778891 chr11:8778883-8778890 chr11:8778882-8778890 chr11:8778881-8778891 chr11:8778878-8778889 chr11:8778881-8778891

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8709205..8712397-chr11:8778361..8782089,3	MCF-7	breast:

Variant related genes	Relation type
ST5	TF binding region
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10160684	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10500705	0.95[CEU][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10500707	0.95[CEU][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10732515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10734636	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10734637	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743089	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10769952	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10769953	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10769954	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10769959	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11042058	0.95[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs11042066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042068	0.95[CEU][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11042077	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs11603335	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2173999	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292045	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2292046	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2873297	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34090393	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34524863	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34599227	0.82[EUR][1000 genomes]
rs35670750	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3763920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3812762	0.86[CEU][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs3842991	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3844099	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3844100	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3850933	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3862352	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4929910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4929931	0.84[EUR][1000 genomes]
rs4929934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4929936	0.95[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6484008	0.91[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6484425	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7120004	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7934519	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7952335	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs905289	0.95[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1079452	SNORA45	cis	cerebellum	SCAN
rs1079452	HBB	cis	cerebellum	SCAN
rs1079452	STK33	cis	cerebellum	SCAN
rs1079452	RPL27A	cis	parietal	SCAN
rs1079452	MRPL17	cis	cerebellum	SCAN
rs1079452	TMEM9B	cis	parietal	SCAN
rs1079452	RPL27A	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8746600-8783000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:8753000-8780600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:8755800-8780800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr11:8763400-8781000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr11:8767000-8779800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:8769400-8781000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr11:8771400-8779600	Weak transcription	Gastric	stomach
8	chr11:8772200-8781200	Weak transcription	Lung	lung
9	chr11:8772200-8782600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr11:8772400-8780400	Weak transcription	Placenta	Placenta
11	chr11:8772400-8782800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:8772400-8787000	Weak transcription	Brain Hippocampus Middle	brain
13	chr11:8772400-8788400	Weak transcription	Hela-S3	cervix
14	chr11:8775400-8780000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr11:8775400-8782800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr11:8776000-8779400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:8776000-8781800	Enhancers	NHDF-Ad	bronchial
18	chr11:8777000-8779400	Enhancers	Osteobl	bone
19	chr11:8777000-8780200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr11:8777000-8781200	Weak transcription	Fetal Lung	lung
21	chr11:8777200-8779200	Enhancers	Right Ventricle	heart
22	chr11:8777200-8779200	Genic enhancers	HSMM	muscle
23	chr11:8777200-8782200	Enhancers	Psoas Muscle	Psoas
24	chr11:8777400-8779200	Enhancers	HSMMtube	muscle
25	chr11:8777400-8779400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr11:8777400-8779600	Enhancers	Adipose Nuclei	Adipose
27	chr11:8777400-8780000	Enhancers	NH-A	brain
28	chr11:8777400-8780200	Enhancers	Pancreas	Pancrea
29	chr11:8777400-8780400	Enhancers	Stomach Smooth Muscle	stomach
30	chr11:8777400-8780600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:8777400-8780600	Enhancers	Colon Smooth Muscle	Colon
32	chr11:8777400-8780600	Enhancers	Fetal Muscle Leg	muscle
33	chr11:8777400-8783400	Enhancers	NHLF	lung
34	chr11:8777400-8784000	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr11:8777400-8784200	Enhancers	Fetal Intestine Large	intestine
36	chr11:8777400-8784200	Enhancers	Left Ventricle	heart
37	chr11:8777400-8795800	Enhancers	Rectal Smooth Muscle	rectum
38	chr11:8777600-8779200	Enhancers	Fetal Stomach	stomach
39	chr11:8777600-8779600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr11:8777600-8780000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr11:8777600-8787800	Weak transcription	Esophagus	oesophagus
42	chr11:8777800-8779400	Enhancers	Placenta Amnion	Placenta Amnion
43	chr11:8777800-8781600	Weak transcription	Liver	Liver
44	chr11:8777800-8781800	Genic enhancers	Fetal Intestine Small	intestine
45	chr11:8777800-8785400	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr11:8778000-8779200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:8778000-8779200	Enhancers	Fetal Heart	heart
48	chr11:8778000-8779400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr11:8778000-8779400	Enhancers	Fetal Muscle Trunk	muscle
50	chr11:8778000-8780000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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