Variant report

Variant	rs10769958
Chromosome Location	chr11:8815115-8815116
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	chr11:8708277..8712745-chr11:8814108..8817920,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10769947	0.96[CEU][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs10769948	0.96[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10769955	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10769957	0.96[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10840147	0.81[CEU][hapmap]
rs11042055	0.92[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs11042059	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11042060	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11042067	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042069	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11603841	0.88[CHB][hapmap]
rs12224436	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12421789	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2316865	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2568090	0.90[CHB][hapmap]
rs2742545	0.81[CEU][hapmap]
rs3763918	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3794153	0.92[CEU][hapmap]
rs4579928	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4929911	0.96[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4929912	0.96[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4929914	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs4929916	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6484484	1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6484496	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7107867	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7129667	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7944560	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs905290	0.92[CEU][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv553447	chr11:8792622-8825966	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10769958	TMEM9B-AS1	cis	lung	GTEx
rs10769958	STK33	cis	cerebellum	SCAN
rs10769958	OR52A1	cis	parietal	SCAN
rs10769958	ST5	cis	parietal	SCAN
rs10769958	NRIP3	cis	parietal	SCAN
rs10769958	RRP8	cis	parietal	SCAN
rs10769958	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs10769958	OR52E8	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8797800-8827200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:8800800-8822400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr11:8800800-8825800	Weak transcription	Brain Angular Gyrus	brain
4	chr11:8800800-8827400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:8801000-8815600	Weak transcription	NHDF-Ad	bronchial
6	chr11:8801600-8820000	Weak transcription	HSMMtube	muscle
7	chr11:8801600-8827400	Weak transcription	Esophagus	oesophagus
8	chr11:8802000-8816000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr11:8802200-8819200	Weak transcription	NH-A	brain
10	chr11:8802800-8816000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:8803000-8815800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:8803000-8820600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:8807600-8815200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:8808200-8815800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:8808600-8819400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr11:8808800-8816000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr11:8808800-8816200	Weak transcription	Brain Hippocampus Middle	brain
18	chr11:8809000-8815800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr11:8809000-8816000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr11:8809000-8816200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr11:8809000-8830200	Weak transcription	Fetal Brain Male	brain
22	chr11:8809200-8815600	Weak transcription	HSMM	muscle
23	chr11:8809200-8815800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr11:8809200-8816200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr11:8809200-8826600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr11:8809200-8829200	Weak transcription	Fetal Kidney	kidney
27	chr11:8809400-8815800	Weak transcription	Placenta	Placenta
28	chr11:8810000-8815800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr11:8810400-8815800	Weak transcription	Spleen	Spleen
30	chr11:8810400-8816200	Weak transcription	NHLF	lung
31	chr11:8810600-8816000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:8810600-8820600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:8811200-8815200	Enhancers	Duodenum Mucosa	Duodenum
34	chr11:8811200-8815800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr11:8811800-8815800	Weak transcription	Ovary	ovary
36	chr11:8811800-8827000	Weak transcription	HMEC	breast
37	chr11:8811800-8828600	Weak transcription	Hela-S3	cervix
38	chr11:8811800-8828800	Weak transcription	Aorta	Aorta
39	chr11:8811800-8830400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr11:8811800-8830600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:8812200-8815800	Weak transcription	Colonic Mucosa	Colon
42	chr11:8812200-8816200	Weak transcription	Fetal Thymus	thymus
43	chr11:8812400-8815800	Weak transcription	Fetal Stomach	stomach
44	chr11:8812400-8815800	Weak transcription	Left Ventricle	heart
45	chr11:8812400-8815800	Weak transcription	Psoas Muscle	Psoas
46	chr11:8812400-8816000	Weak transcription	Fetal Heart	heart
47	chr11:8812400-8820600	Weak transcription	Right Ventricle	heart
48	chr11:8812800-8815200	Weak transcription	Fetal Intestine Large	intestine
49	chr11:8812800-8815200	Weak transcription	Small Intestine	intestine
50	chr11:8812800-8815800	Weak transcription	Lung	lung

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