Variant report

Variant	rs28557406
Chromosome Location	chr15:42830307-42830308
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	chr15:42829023..42831812-chr15:42840835..42842779,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180979	Chromatin interaction
ENSG00000137814	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs28491449	0.87[AMR][1000 genomes]
rs28548127	0.87[AMR][1000 genomes]
rs28599675	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28646241	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28882725	0.87[AMR][1000 genomes]
rs9919987	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42793000-42835600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:42793800-42837200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:42797400-42839800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:42797600-42839400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:42799200-42839400	Weak transcription	Stomach Mucosa	stomach
6	chr15:42802400-42839200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:42803200-42837200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:42803600-42839400	Weak transcription	A549	lung
9	chr15:42804600-42836400	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr15:42804800-42836400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr15:42804800-42836400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr15:42805400-42836800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:42806200-42836400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:42806200-42839000	Weak transcription	Fetal Brain Male	brain
15	chr15:42808400-42839000	Weak transcription	Fetal Heart	heart
16	chr15:42808800-42836000	Weak transcription	Esophagus	oesophagus
17	chr15:42810200-42831000	Weak transcription	Gastric	stomach
18	chr15:42810200-42840200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:42811000-42837600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr15:42811200-42831200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:42811800-42836000	Weak transcription	Colonic Mucosa	Colon
22	chr15:42815800-42833000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr15:42817400-42840200	Weak transcription	Pancreas	Pancrea
24	chr15:42820000-42831400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:42820200-42831600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:42820600-42831000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr15:42821000-42832200	Strong transcription	Adipose Nuclei	Adipose
28	chr15:42821200-42836200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:42821200-42839800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr15:42821400-42831400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:42821400-42832000	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr15:42822000-42831600	Strong transcription	Brain Hippocampus Middle	brain
33	chr15:42822000-42832800	Strong transcription	Fetal Brain Female	brain
34	chr15:42822200-42840200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr15:42822800-42840000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr15:42823000-42835600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr15:42823200-42830600	Weak transcription	Fetal Intestine Small	intestine
38	chr15:42823400-42830600	Weak transcription	NHEK	skin
39	chr15:42823400-42840200	Weak transcription	Psoas Muscle	Psoas
40	chr15:42823800-42835600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr15:42823800-42835600	Weak transcription	NHLF	lung
42	chr15:42823800-42838000	Weak transcription	Brain Angular Gyrus	brain
43	chr15:42824000-42830600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr15:42824000-42830800	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr15:42824000-42831200	Weak transcription	Fetal Lung	lung
46	chr15:42824000-42834200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr15:42824000-42835000	Weak transcription	Spleen	Spleen
48	chr15:42824000-42840200	Weak transcription	Small Intestine	intestine
49	chr15:42824200-42832400	Weak transcription	Colon Smooth Muscle	Colon
50	chr15:42824200-42835800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links