Variant report

Variant	rs10743089
Chromosome Location	chr11:8788168-8788169
allele	A/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	RAD21	chr11:8787751-8788175	H1-hESC	embryonic stem cell:	n/a	n/a
2	CREB1	chr11:8787832-8788539	H1-hESC	embryonic stem cell:	n/a	n/a
3	ATF1	chr11:8788102-8788368	K562	blood:	n/a	n/a
4	CREB1	chr11:8788055-8788416	GM12878	blood:	n/a	n/a
5	CREB1	chr11:8787989-8788523	H1-hESC	embryonic stem cell:	n/a	n/a
6	CREB1	chr11:8788006-8788510	HepG2	liver:	n/a	n/a
7	HDAC2	chr11:8787897-8788454	H1-hESC	embryonic stem cell:	n/a	n/a
8	JUND	chr11:8788037-8788492	H1-hESC	embryonic stem cell:	n/a	chr11:8788433-8788443 chr11:8788432-8788444 chr11:8788433-8788443 chr11:8788434-8788442 chr11:8788433-8788443
9	CREB1	chr11:8787930-8788618	K562	blood:	n/a	n/a
10	CTCF	chr11:8787869-8788174	K562	blood:	n/a	chr11:8788017-8788026

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
ENSG00000255159	TF binding region
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10160684	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10500705	0.95[CEU][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10500707	0.95[CEU][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10732515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10734636	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10734637	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743087	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]
rs10743088	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	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10769953	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.98[ASN][1000 genomes]
rs10769954	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10769959	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1079452	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]
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];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042068	0.95[CEU][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11042077	0.87[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs11603335	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[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];0.99[ASN][1000 genomes]
rs2292045	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2292046	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2873297	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34090393	0.81[AMR][1000 genomes];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]
rs3751071	0.81[AMR][1000 genomes]
rs3763920	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];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3812762	0.86[CEU][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs3842991	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3844099	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3844100	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3850933	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3862352	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3913547	0.93[LWK][hapmap];0.85[MKK][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs4929910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4929931	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4929934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6484425	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7120004	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.88[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];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7952335	0.89[CEU][hapmap];0.84[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];0.84[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
rs10743089	TMEM9B	cis	parietal	SCAN
rs10743089	RPL27A	cis	parietal	SCAN
rs10743089	RPL27A	cis	cerebellum	SCAN
rs10743089	SNORA45	cis	cerebellum	SCAN
rs10743089	STK33	cis	cerebellum	SCAN
rs10743089	HBB	cis	cerebellum	SCAN
rs10743089	MRPL17	cis	cerebellum	SCAN

Chromatin state (count:94 , 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	chr11:8779600-8799600	Weak transcription	Fetal Brain Male	brain
4	chr11:8780000-8792400	Weak transcription	HepG2	liver
5	chr11:8781400-8794600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr11:8782000-8791600	Enhancers	Colon Smooth Muscle	Colon
7	chr11:8783200-8790000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr11:8783800-8788200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr11:8783800-8788400	Weak transcription	Fetal Lung	lung
10	chr11:8783800-8788800	Weak transcription	Fetal Kidney	kidney
11	chr11:8784000-8788200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr11:8784000-8788400	Weak transcription	Brain Anterior Caudate	brain
13	chr11:8784000-8788600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr11:8784000-8790200	Weak transcription	Small Intestine	intestine
15	chr11:8784000-8794200	Weak transcription	Colonic Mucosa	Colon
16	chr11:8785000-8788600	Enhancers	HSMMtube	muscle
17	chr11:8785000-8791400	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr11:8785200-8799400	Enhancers	Fetal Heart	heart
19	chr11:8785400-8788400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr11:8786000-8788800	Enhancers	Pancreas	Pancrea
21	chr11:8786200-8788400	Weak transcription	Placenta	Placenta
22	chr11:8786400-8794200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:8786600-8788200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr11:8786600-8788200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr11:8786600-8788200	Enhancers	Gastric	stomach
26	chr11:8786600-8788400	Enhancers	HMEC	breast
27	chr11:8786600-8788400	Enhancers	Osteobl	bone
28	chr11:8786600-8788600	Enhancers	NH-A	brain
29	chr11:8786600-8789000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr11:8786600-8789000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr11:8786600-8789200	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr11:8786600-8789400	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr11:8786600-8789600	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr11:8786600-8789800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr11:8786600-8790400	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr11:8786600-8790400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr11:8786600-8791200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr11:8786600-8791200	Enhancers	Placenta Amnion	Placenta Amnion
39	chr11:8786600-8791400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr11:8786600-8791400	Enhancers	Right Ventricle	heart
41	chr11:8786600-8791600	Enhancers	Left Ventricle	heart
42	chr11:8786600-8791800	Enhancers	NHDF-Ad	bronchial
43	chr11:8786600-8791800	Enhancers	NHLF	lung
44	chr11:8786600-8795400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr11:8786600-8795400	Enhancers	Stomach Mucosa	stomach
46	chr11:8786600-8798000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:8786600-8803000	Enhancers	Ovary	ovary
48	chr11:8786800-8788800	Enhancers	H1 Cell Line	embryonic stem cell
49	chr11:8786800-8788800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:8786800-8788800	Enhancers	HUES64 Cell Line	embryonic stem cell

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