Variant report

Variant	rs12799145
Chromosome Location	chr11:58940435-58940436
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58940155..58942428-chr11:58942468..58945192,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10128635	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10128647	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10128699	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10792222	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10792223	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10792224	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10792225	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10792226	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10896938	0.80[EUR][1000 genomes]
rs10896940	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10896944	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10896945	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10896946	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10896947	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11229861	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12286883	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12291322	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12796683	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2154629	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2839968	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4938910	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73476933	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv3427190	chr11:58938601-58941149	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	esv3399192	chr11:58938776-58941074	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58938600-58942000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr11:58938800-58941200	Active TSS	Brain Cingulate Gyrus	brain
3	chr11:58938800-58941400	Active TSS	Brain Anterior Caudate	brain
4	chr11:58938800-58941800	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr11:58939000-58940600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr11:58939000-58940600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:58939000-58940800	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr11:58939000-58940800	Active TSS	Muscle Satellite Cultured Cells	--
9	chr11:58939000-58941000	Active TSS	Hela-S3	cervix
10	chr11:58939000-58941200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:58939000-58941200	Active TSS	A549	lung
12	chr11:58939000-58941400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:58939000-58941400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:58939000-58941400	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr11:58939000-58941400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:58939000-58941400	Active TSS	Brain Substantia Nigra	brain
17	chr11:58939000-58941400	Active TSS	Fetal Intestine Small	intestine
18	chr11:58939000-58941400	Active TSS	Fetal Lung	lung
19	chr11:58939000-58941400	Active TSS	Gastric	stomach
20	chr11:58939000-58941400	Active TSS	Placenta Amnion	Placenta Amnion
21	chr11:58939000-58941400	Active TSS	Psoas Muscle	Psoas
22	chr11:58939000-58941600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr11:58939000-58941600	Active TSS	H9 Cell Line	embryonic stem cell
24	chr11:58939000-58941600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:58939000-58941600	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr11:58939000-58941600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr11:58939000-58941600	Active TSS	Esophagus	oesophagus
28	chr11:58939000-58941600	Active TSS	Fetal Intestine Large	intestine
29	chr11:58939000-58941600	Active TSS	Fetal Kidney	kidney
30	chr11:58939000-58941600	Active TSS	Ovary	ovary
31	chr11:58939000-58941600	Active TSS	HSMM	muscle
32	chr11:58939000-58941600	Active TSS	HSMMtube	muscle
33	chr11:58939000-58941600	Active TSS	NHDF-Ad	bronchial
34	chr11:58939000-58941800	Active TSS	Colon Smooth Muscle	Colon
35	chr11:58939000-58942000	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr11:58939000-58942400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr11:58939000-58942600	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr11:58939200-58941200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr11:58939200-58941200	Active TSS	Aorta	Aorta
40	chr11:58939200-58941600	Active TSS	Small Intestine	intestine
41	chr11:58939200-58941800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr11:58939200-58941800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:58939400-58940800	Active TSS	GM12878-XiMat	blood
44	chr11:58939400-58941400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:58939400-58941400	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr11:58939400-58941600	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr11:58939400-58942000	Active TSS	Duodenum Mucosa	Duodenum
48	chr11:58940000-58940600	Flanking Active TSS	Lung	lung
49	chr11:58940000-58940600	Flanking Bivalent TSS/Enh	Osteobl	bone
50	chr11:58940000-58940800	Flanking Active TSS	Dnd41	blood

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