Variant report

Variant	rs1228053
Chromosome Location	chr11:48056130-48056131
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:48051913..48054330-chr11:48054555..48057402,3	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10466481	0.93[AFR][1000 genomes]
rs11039502	0.93[AFR][1000 genomes]
rs12275949	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12278732	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228046	1.00[EUR][1000 genomes]
rs1228047	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228048	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228050	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12280964	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12281120	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12282774	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12287023	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12290438	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7129454	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv1053145	chr11:47967902-48086950	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv870381	chr11:47989434-48142648	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
11	esv3396029	chr11:47993857-48241494	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
12	nsv897327	chr11:48004369-48911660	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv869124	chr11:48014539-48783113	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv1051805	chr11:48016488-48378048	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
15	nsv428573	chr11:48032457-48152344	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
16	nsv897328	chr11:48043053-48901553	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv897329	chr11:48052676-48319974	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:48035600-48056600	Weak transcription	HSMM	muscle
2	chr11:48046400-48056600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:48046400-48058200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr11:48046600-48059600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr11:48047000-48057800	Weak transcription	NHLF	lung
6	chr11:48047400-48073400	Weak transcription	HSMMtube	muscle
7	chr11:48047400-48073800	Weak transcription	Left Ventricle	heart
8	chr11:48048000-48056600	Weak transcription	Pancreas	Pancrea
9	chr11:48048000-48057200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr11:48049000-48058600	Genic enhancers	A549	lung
11	chr11:48049400-48056600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr11:48050200-48068200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr11:48050400-48058000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr11:48050800-48056800	Weak transcription	Small Intestine	intestine
15	chr11:48050800-48058000	Enhancers	Adipose Nuclei	Adipose
16	chr11:48050800-48058600	Enhancers	Brain Anterior Caudate	brain
17	chr11:48050800-48073000	Weak transcription	Esophagus	oesophagus
18	chr11:48051000-48056600	Weak transcription	Brain Germinal Matrix	brain
19	chr11:48051000-48057200	Weak transcription	Fetal Heart	heart
20	chr11:48051600-48057600	Weak transcription	Fetal Lung	lung
21	chr11:48051600-48071200	Weak transcription	Fetal Intestine Large	intestine
22	chr11:48051600-48073800	Weak transcription	Aorta	Aorta
23	chr11:48051800-48057200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr11:48051800-48057200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:48051800-48057200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr11:48051800-48057400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:48051800-48058600	Enhancers	Primary T cells fromperipheralblood	blood
28	chr11:48052000-48056200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr11:48052000-48056600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr11:48052000-48057000	Strong transcription	Fetal Intestine Small	intestine
31	chr11:48052600-48060000	Enhancers	Brain Substantia Nigra	brain
32	chr11:48052800-48057000	Enhancers	Liver	Liver
33	chr11:48052800-48058000	Enhancers	Fetal Thymus	thymus
34	chr11:48052800-48059200	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr11:48053000-48056800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr11:48053200-48056200	Weak transcription	Fetal Stomach	stomach
37	chr11:48053200-48056600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr11:48053200-48057800	Weak transcription	Fetal Kidney	kidney
39	chr11:48053200-48060000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:48053400-48057400	Enhancers	Brain Hippocampus Middle	brain
41	chr11:48053600-48056400	Weak transcription	NHDF-Ad	bronchial
42	chr11:48053600-48056600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr11:48053600-48056800	Weak transcription	Osteobl	bone
44	chr11:48053600-48057200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr11:48053600-48057600	Enhancers	Primary hematopoietic stem cells	blood
46	chr11:48053600-48065400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr11:48053600-48065800	Weak transcription	Colonic Mucosa	Colon
48	chr11:48053800-48056200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr11:48053800-48056200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr11:48053800-48056400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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