Variant report

Variant	rs2899043
Chromosome Location	chr15:42554673-42554674
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	chr15:42553565..42555968-chr15:42563813..42566257,3	MCF-7	breast:
2	chr15:42552126..42554806-chr15:42568266..42570874,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214013	Chromatin interaction
ENSG00000103978	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11070368	0.85[AFR][1000 genomes]
rs11858453	0.85[AFR][1000 genomes]
rs12913755	0.85[AFR][1000 genomes]
rs2412677	0.85[AFR][1000 genomes]
rs2412679	0.83[EUR][1000 genomes]
rs2412680	0.84[AFR][1000 genomes]
rs2412681	0.85[AFR][1000 genomes]
rs6493028	0.85[AFR][1000 genomes]
rs6493029	0.85[AFR][1000 genomes]
rs8038978	0.93[AFR][1000 genomes]
rs8040580	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][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	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv1807328	chr15:42525300-42573278	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv904133	chr15:42528982-42681057	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 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	chr15:42500800-42563200	Weak transcription	Stomach Mucosa	stomach
2	chr15:42519400-42562800	Weak transcription	Fetal Heart	heart
3	chr15:42520200-42561000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:42542800-42561600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:42543400-42559000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr15:42543400-42561200	Strong transcription	Liver	Liver
7	chr15:42543600-42561000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:42543800-42556600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:42543800-42557000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:42543800-42560200	Strong transcription	Duodenum Mucosa	Duodenum
11	chr15:42543800-42560800	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr15:42543800-42561600	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr15:42544000-42560600	Strong transcription	Adipose Nuclei	Adipose
14	chr15:42544000-42560800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr15:42544200-42561000	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr15:42544200-42561200	Strong transcription	Primary B cells from peripheral blood	blood
17	chr15:42544200-42561200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr15:42544200-42561800	Strong transcription	Osteobl	bone
19	chr15:42544400-42561200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:42544400-42561200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:42544600-42557800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr15:42544600-42560600	Strong transcription	Placenta	Placenta
23	chr15:42544600-42560800	Strong transcription	Fetal Thymus	thymus
24	chr15:42544600-42561600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:42544800-42559800	Strong transcription	Fetal Kidney	kidney
26	chr15:42544800-42560800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:42545000-42561400	Strong transcription	HSMM	muscle
28	chr15:42545200-42560600	Strong transcription	HepG2	liver
29	chr15:42545200-42560800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:42545400-42560400	Strong transcription	Primary T cells from cord blood	blood
31	chr15:42545400-42560400	Strong transcription	Stomach Smooth Muscle	stomach
32	chr15:42545400-42560800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:42545600-42559400	Strong transcription	Fetal Muscle Leg	muscle
34	chr15:42545600-42563400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr15:42545800-42558600	Strong transcription	Primary B cells from cord blood	blood
36	chr15:42545800-42560400	Strong transcription	Fetal Intestine Large	intestine
37	chr15:42545800-42561400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr15:42546000-42560800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:42546000-42564600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr15:42546200-42558400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr15:42546200-42564600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr15:42546400-42559200	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:42546400-42561000	Strong transcription	Dnd41	blood
44	chr15:42546600-42560800	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr15:42546600-42561600	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr15:42546800-42559400	Strong transcription	Fetal Muscle Trunk	muscle
47	chr15:42546800-42560800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr15:42547000-42564200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr15:42547200-42556000	Strong transcription	Fetal Stomach	stomach
50	chr15:42547400-42559200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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