Variant report

Variant	rs11574099
Chromosome Location	chr12:48248299-48248300
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	chr12:48213191..48215261-chr12:48247423..48250020,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000061273	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11574103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11574114	0.80[EUR][1000 genomes]
rs11574119	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11574139	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2853563	0.83[EUR][1000 genomes]
rs3858733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55748765	0.80[EUR][1000 genomes]
rs58789572	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv1048466	chr12:48195350-48262541	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
4	nsv541488	chr12:48195350-48262541	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48227200-48261200	Weak transcription	HSMM	muscle
2	chr12:48231400-48261400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr12:48232200-48253000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:48232400-48263800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:48232400-48276600	Weak transcription	Pancreas	Pancrea
6	chr12:48233000-48275200	Weak transcription	Hela-S3	cervix
7	chr12:48234600-48252400	Weak transcription	Stomach Mucosa	stomach
8	chr12:48236400-48252000	Strong transcription	Fetal Intestine Small	intestine
9	chr12:48236600-48259400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr12:48237000-48252200	Strong transcription	Duodenum Mucosa	Duodenum
11	chr12:48237000-48253200	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr12:48237000-48259000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:48237000-48261800	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr12:48237400-48252600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr12:48237400-48261200	Weak transcription	NH-A	brain
16	chr12:48238600-48253400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:48240000-48261200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:48240400-48250600	Weak transcription	Aorta	Aorta
19	chr12:48240600-48250600	Weak transcription	NHDF-Ad	bronchial
20	chr12:48240800-48250600	Weak transcription	Gastric	stomach
21	chr12:48241200-48263800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:48243400-48263600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:48244000-48250400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:48244000-48253400	Strong transcription	Osteobl	bone
25	chr12:48244200-48251600	Weak transcription	Primary T cells from cord blood	blood
26	chr12:48244200-48252000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:48244200-48252600	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr12:48244400-48252000	Strong transcription	NHEK	skin
29	chr12:48244400-48252600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:48245400-48250400	Weak transcription	Spleen	Spleen
31	chr12:48245400-48252400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:48245400-48274000	Weak transcription	Small Intestine	intestine
33	chr12:48246200-48252000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:48246200-48261200	Weak transcription	Placenta	Placenta
35	chr12:48246400-48250600	Weak transcription	Esophagus	oesophagus
36	chr12:48246400-48257400	Weak transcription	GM12878-XiMat	blood
37	chr12:48246400-48261600	Weak transcription	Primary B cells from cord blood	blood
38	chr12:48246400-48263800	Weak transcription	Right Atrium	heart
39	chr12:48246600-48250400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr12:48246600-48250600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:48246600-48261800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr12:48246800-48248400	Weak transcription	Colonic Mucosa	Colon
43	chr12:48246800-48248400	Weak transcription	Fetal Stomach	stomach
44	chr12:48246800-48250800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr12:48246800-48251800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:48246800-48252800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:48246800-48258000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:48246800-48259000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:48247000-48248400	Weak transcription	Liver	Liver
50	chr12:48247000-48249800	Weak transcription	HepG2	liver

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