Variant report

Variant	rs10743087
Chromosome Location	chr11:8786058-8786059
allele	C/T
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:
2	chr11:8775891..8778545-chr11:8784812..8786511,2	K562	blood:

Variant related genes	Relation type
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10160684	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10500705	0.95[CEU][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs10500707	0.95[CEU][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10732515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10734636	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10734637	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743088	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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10769952	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769953	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10769954	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769959	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1079452	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]
rs11042058	0.95[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs11042066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11042068	0.95[CEU][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs11042077	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs11603335	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12420964	0.83[LWK][hapmap]
rs2173999	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292045	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs2292046	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2873297	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34090393	0.86[EUR][1000 genomes]
rs34524863	0.90[EUR][1000 genomes]
rs34599227	0.82[EUR][1000 genomes]
rs35670750	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3763920	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];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3812762	0.86[CEU][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs3842991	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3844099	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3844100	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3850933	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3862352	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3913547	0.93[LWK][hapmap];0.84[MKK][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs4929910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4929931	0.83[EUR][1000 genomes]
rs4929934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4929936	0.95[CEU][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs6484008	0.91[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs6484425	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7120004	0.91[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7934519	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7952335	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs905289	0.95[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.85[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10743087	TMEM9B	cis	parietal	SCAN
rs10743087	HBB	cis	cerebellum	SCAN
rs10743087	RPL27A	cis	parietal	SCAN
rs10743087	RPL27A	cis	cerebellum	SCAN
rs10743087	SNORA45	cis	cerebellum	SCAN
rs10743087	STK33	cis	cerebellum	SCAN
rs10743087	MRPL17	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8772400-8787000	Weak transcription	Brain Hippocampus Middle	brain
2	chr11:8772400-8788400	Weak transcription	Hela-S3	cervix
3	chr11:8777400-8795800	Enhancers	Rectal Smooth Muscle	rectum
4	chr11:8777600-8787800	Weak transcription	Esophagus	oesophagus
5	chr11:8779200-8786600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:8779400-8786600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:8779400-8787000	Weak transcription	NHEK	skin
8	chr11:8779600-8786600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr11:8779600-8799600	Weak transcription	Fetal Brain Male	brain
10	chr11:8780000-8786600	Weak transcription	HMEC	breast
11	chr11:8780000-8792400	Weak transcription	HepG2	liver
12	chr11:8781000-8786800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr11:8781400-8786600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:8781400-8787800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:8781400-8794600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr11:8781600-8786600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:8781800-8786600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:8781800-8786600	Weak transcription	NHDF-Ad	bronchial
19	chr11:8782000-8787200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr11:8782000-8791600	Enhancers	Colon Smooth Muscle	Colon
21	chr11:8782200-8786800	Weak transcription	Aorta	Aorta
22	chr11:8783000-8786600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr11:8783200-8786600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:8783200-8786600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr11:8783200-8786600	Weak transcription	NH-A	brain
26	chr11:8783200-8790000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr11:8783400-8786600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr11:8783400-8786600	Weak transcription	NHLF	lung
29	chr11:8783400-8786800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr11:8783600-8787000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr11:8783800-8787800	Weak transcription	Liver	Liver
32	chr11:8783800-8788000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr11:8783800-8788000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr11:8783800-8788200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr11:8783800-8788400	Weak transcription	Fetal Lung	lung
36	chr11:8783800-8788800	Weak transcription	Fetal Kidney	kidney
37	chr11:8784000-8786600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:8784000-8786600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr11:8784000-8786600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr11:8784000-8786600	Weak transcription	Gastric	stomach
41	chr11:8784000-8786600	Weak transcription	Right Atrium	heart
42	chr11:8784000-8786600	Weak transcription	Right Ventricle	heart
43	chr11:8784000-8786600	Weak transcription	Stomach Mucosa	stomach
44	chr11:8784000-8786800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr11:8784000-8786800	Weak transcription	Brain Angular Gyrus	brain
46	chr11:8784000-8786800	Weak transcription	Lung	lung
47	chr11:8784000-8786800	Weak transcription	Spleen	Spleen
48	chr11:8784000-8787000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr11:8784000-8787600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr11:8784000-8788000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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