Variant report

Variant	rs11039080
Chromosome Location	chr11:47093084-47093085
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	chr11:47085147..47087563-chr11:47092809..47094555,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10501319	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10742797	0.81[ASN][1000 genomes]
rs10769225	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10769226	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10769227	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10769228	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10769248	0.82[ASN][1000 genomes]
rs10838635	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10838640	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10838641	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10838644	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10838646	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10838652	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10838658	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10838662	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10838663	0.92[ASN][1000 genomes]
rs10838664	0.88[ASN][1000 genomes]
rs11039028	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11039033	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11039057	0.82[ASN][1000 genomes]
rs11039081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039098	0.84[ASN][1000 genomes]
rs11600292	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11601798	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11602250	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11603373	0.89[ASN][1000 genomes]
rs11608083	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12417519	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12574410	0.92[ASN][1000 genomes]
rs17790204	0.85[ASN][1000 genomes]
rs2087215	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2279438	0.87[ASN][1000 genomes]
rs2279439	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34340483	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3758666	0.81[ASN][1000 genomes]
rs3922684	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4269876	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4315028	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4394802	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4494268	0.89[ASN][1000 genomes]
rs4498951	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4528282	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4548577	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4576779	0.95[ASN][1000 genomes]
rs4581406	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4587689	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4752815	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4752816	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4752965	0.92[ASN][1000 genomes]
rs4752968	0.83[ASN][1000 genomes]
rs4752969	0.92[ASN][1000 genomes]
rs61896133	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61896136	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61897787	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61897844	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61897857	0.81[ASN][1000 genomes]
rs6485715	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6485716	0.85[ASN][1000 genomes]
rs6485726	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7108822	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7111270	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7112854	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7113108	0.91[AFR][1000 genomes]
rs7114683	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7123632	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7124648	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7126005	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7127741	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7128193	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7128650	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7130006	0.85[ASN][1000 genomes]
rs7130947	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7929688	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7935346	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7937410	0.88[ASN][1000 genomes]
rs7938169	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7939786	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7940240	0.89[ASN][1000 genomes]
rs7945558	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7946739	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7950753	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7951979	0.88[ASN][1000 genomes]
rs901747	0.88[ASN][1000 genomes]
rs923324	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043108	chr11:47041565-47117248	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47073800-47100200	Weak transcription	Thymus	Thymus
2	chr11:47075200-47093400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr11:47075800-47093400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr11:47077600-47113200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:47078000-47097000	Weak transcription	Aorta	Aorta
6	chr11:47078200-47093200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:47080600-47093200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:47080800-47103000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:47083200-47100600	Weak transcription	NH-A	brain
10	chr11:47084600-47093400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr11:47084600-47093400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr11:47084600-47093400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr11:47084600-47093400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr11:47084600-47098400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:47085800-47102400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr11:47089200-47093200	Weak transcription	NHEK	skin
17	chr11:47089200-47093400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr11:47089200-47093400	Weak transcription	HSMM	muscle
19	chr11:47089400-47097000	Weak transcription	Gastric	stomach
20	chr11:47089400-47107000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:47089400-47120800	Weak transcription	Hela-S3	cervix
22	chr11:47090000-47096000	Weak transcription	Pancreas	Pancrea
23	chr11:47091600-47094000	Enhancers	Fetal Muscle Leg	muscle
24	chr11:47091600-47095000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr11:47092000-47093800	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr11:47092000-47094000	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr11:47092200-47093200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr11:47092200-47093600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr11:47092200-47093800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr11:47092200-47093800	Enhancers	Placenta	Placenta
31	chr11:47092400-47093400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr11:47092400-47093400	Enhancers	Stomach Smooth Muscle	stomach
33	chr11:47092400-47093600	Enhancers	Fetal Intestine Small	intestine
34	chr11:47092400-47093600	Enhancers	HSMMtube	muscle
35	chr11:47092400-47093800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr11:47092400-47093800	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr11:47092400-47093800	Enhancers	Fetal Intestine Large	intestine
38	chr11:47092400-47093800	Enhancers	Small Intestine	intestine
39	chr11:47092400-47094000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:47092400-47094000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr11:47092400-47094000	Enhancers	Brain Cingulate Gyrus	brain
42	chr11:47092400-47094000	Enhancers	Duodenum Mucosa	Duodenum
43	chr11:47092400-47094000	Enhancers	Fetal Stomach	stomach
44	chr11:47092600-47093400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr11:47092600-47093600	Enhancers	Stomach Mucosa	stomach
46	chr11:47092600-47093800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr11:47092800-47093200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr11:47092800-47093400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr11:47092800-47093600	Enhancers	Brain Angular Gyrus	brain
50	chr11:47092800-47094000	Enhancers	A549	lung

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