Variant report

Variant	rs28869227
Chromosome Location	chr15:40481652-40481653
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40466317..40467949-chr15:40479738..40482737,2	MCF-7	breast:
2	chr15:40476784..40479145-chr15:40481469..40483471,2	K562	blood:
3	chr15:40475654..40478286-chr15:40479648..40481857,2	K562	blood:

Variant related genes	Relation type
ENSG00000156970	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11070254	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070255	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12102172	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12385956	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13380113	1.00[EUR][1000 genomes]
rs13380241	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1494534	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1801528	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1869906	1.00[EUR][1000 genomes]
rs28390245	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28417868	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28418337	0.87[AMR][1000 genomes]
rs28485685	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28501335	1.00[EUR][1000 genomes]
rs28526743	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28561898	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28565228	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28606396	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28637656	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28637697	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28657938	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28668026	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28673302	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28744626	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28750294	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28792493	1.00[EUR][1000 genomes]
rs28844897	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35611758	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55984256	1.00[EUR][1000 genomes]
rs56010221	1.00[EUR][1000 genomes]
rs56888636	1.00[EUR][1000 genomes]
rs57029027	1.00[EUR][1000 genomes]
rs58216655	1.00[EUR][1000 genomes]
rs58355728	0.87[AMR][1000 genomes]
rs58584688	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58870954	1.00[EUR][1000 genomes]
rs60743501	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60889301	1.00[EUR][1000 genomes]
rs61579851	1.00[EUR][1000 genomes]
rs6492943	1.00[EUR][1000 genomes]
rs7164281	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7168394	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7168416	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7173239	1.00[EUR][1000 genomes]
rs7175153	1.00[EUR][1000 genomes]
rs7178873	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73377835	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389487	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389489	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389492	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389507	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389520	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389531	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389536	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389540	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390146	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390155	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390162	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390167	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390168	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390187	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73391309	0.87[AMR][1000 genomes]
rs73391316	0.87[AMR][1000 genomes]
rs73392641	1.00[EUR][1000 genomes]
rs8023956	1.00[EUR][1000 genomes]
rs8026988	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8364	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9672591	1.00[EUR][1000 genomes]
rs967945	0.87[AMR][1000 genomes]
rs9806126	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9806144	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40453800-40525000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:40454000-40515200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:40454600-40502400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr15:40454800-40524200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:40455400-40530400	Weak transcription	Fetal Brain Female	brain
6	chr15:40455600-40518200	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:40455600-40522200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:40455600-40530400	Weak transcription	Brain Germinal Matrix	brain
9	chr15:40456200-40524000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr15:40456200-40524000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:40461600-40486800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:40462800-40482200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:40463800-40482000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:40463800-40482600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:40464000-40485000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:40464000-40490200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr15:40465000-40489600	Weak transcription	Fetal Intestine Large	intestine
18	chr15:40468400-40485800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:40469000-40482600	Weak transcription	NHDF-Ad	bronchial
20	chr15:40471400-40517600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:40471400-40524400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:40473200-40517800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr15:40473600-40487400	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr15:40473600-40525200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:40474200-40483000	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr15:40474200-40485000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:40474400-40485400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:40474800-40482800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr15:40475000-40491600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr15:40475000-40526400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr15:40475400-40488800	Weak transcription	NH-A	brain
32	chr15:40475400-40522600	Strong transcription	Dnd41	blood
33	chr15:40475600-40490000	Strong transcription	Fetal Thymus	thymus
34	chr15:40475800-40483600	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr15:40476200-40489400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr15:40476400-40483400	Strong transcription	Fetal Stomach	stomach
37	chr15:40476600-40490000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:40476800-40491600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr15:40477000-40482600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:40477200-40481800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:40477200-40482000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:40477200-40485200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr15:40477800-40483000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr15:40478000-40482600	Weak transcription	Fetal Muscle Leg	muscle
45	chr15:40478000-40482600	Weak transcription	NHLF	lung
46	chr15:40478000-40489600	Weak transcription	Primary B cells from cord blood	blood
47	chr15:40478400-40481800	Weak transcription	HMEC	breast
48	chr15:40478400-40482600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr15:40478400-40482600	Weak transcription	HSMM	muscle
50	chr15:40478400-40482800	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links