Variant report

Variant	rs10743088
Chromosome Location	chr11:8787620-8787621
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8708222..8712147-chr11:8785051..8789387,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:42)

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];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10500705	0.95[CEU][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10500707	0.95[CEU][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10732515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10734636	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10734637	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10743087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10743089	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10769952	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10769953	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10769954	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10769959	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1079452	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]
rs11042058	0.95[CEU][hapmap];0.91[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];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11042068	0.95[CEU][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11042077	0.83[MEX][hapmap]
rs11603335	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2173999	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2292045	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2292046	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2873297	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34090393	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34524863	0.87[EUR][1000 genomes]
rs35670750	0.87[EUR][1000 genomes]
rs3763920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3812762	0.86[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs3842991	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3844099	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3844100	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3850933	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3862352	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4929910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4929931	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4929934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4929936	0.95[CEU][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6484008	0.91[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6484425	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7120004	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7934519	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7952335	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs905289	0.95[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10743088	RPL27A	cis	brain	BrainEAC
rs10743088	RPL27A	cis	parietal	SCAN
rs10743088	RPL27A	cis	frontal cortex	BrainEAC
rs10743088	MRPL17	cis	cerebellum	SCAN
rs10743088	STK33	cis	cerebellum	SCAN
rs10743088	RPL27A	cis	cerebellum	SCAN
rs10743088	SNORA45	cis	cerebellum	SCAN
rs10743088	HBB	cis	cerebellum	SCAN
rs10743088	OR51F1	cis	parietal	SCAN
rs10743088	RPL27A	cis	temporal cortex	BrainEAC
rs10743088	TMEM9B	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8772400-8788400	Weak transcription	Hela-S3	cervix
2	chr11:8777400-8795800	Enhancers	Rectal Smooth Muscle	rectum
3	chr11:8777600-8787800	Weak transcription	Esophagus	oesophagus
4	chr11:8779600-8799600	Weak transcription	Fetal Brain Male	brain
5	chr11:8780000-8792400	Weak transcription	HepG2	liver
6	chr11:8781400-8787800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:8781400-8794600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr11:8782000-8791600	Enhancers	Colon Smooth Muscle	Colon
9	chr11:8783200-8790000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr11:8783800-8787800	Weak transcription	Liver	Liver
11	chr11:8783800-8788000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr11:8783800-8788000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr11:8783800-8788200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr11:8783800-8788400	Weak transcription	Fetal Lung	lung
15	chr11:8783800-8788800	Weak transcription	Fetal Kidney	kidney
16	chr11:8784000-8788000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:8784000-8788000	Weak transcription	Brain Substantia Nigra	brain
18	chr11:8784000-8788200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr11:8784000-8788400	Weak transcription	Brain Anterior Caudate	brain
20	chr11:8784000-8788600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr11:8784000-8790200	Weak transcription	Small Intestine	intestine
22	chr11:8784000-8794200	Weak transcription	Colonic Mucosa	Colon
23	chr11:8784400-8788000	Weak transcription	Psoas Muscle	Psoas
24	chr11:8785000-8788600	Enhancers	HSMMtube	muscle
25	chr11:8785000-8791400	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr11:8785200-8799400	Enhancers	Fetal Heart	heart
27	chr11:8785400-8788400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr11:8786000-8788800	Enhancers	Pancreas	Pancrea
29	chr11:8786200-8788400	Weak transcription	Placenta	Placenta
30	chr11:8786400-8794200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr11:8786600-8788200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr11:8786600-8788200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:8786600-8788200	Enhancers	Gastric	stomach
34	chr11:8786600-8788400	Enhancers	HMEC	breast
35	chr11:8786600-8788400	Enhancers	Osteobl	bone
36	chr11:8786600-8788600	Enhancers	NH-A	brain
37	chr11:8786600-8789000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr11:8786600-8789000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr11:8786600-8789200	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr11:8786600-8789400	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr11:8786600-8789600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr11:8786600-8789800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr11:8786600-8790400	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr11:8786600-8790400	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr11:8786600-8791200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr11:8786600-8791200	Enhancers	Placenta Amnion	Placenta Amnion
47	chr11:8786600-8791400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:8786600-8791400	Enhancers	Right Ventricle	heart
49	chr11:8786600-8791600	Enhancers	Left Ventricle	heart
50	chr11:8786600-8791800	Enhancers	NHDF-Ad	bronchial

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