Variant report

Variant	rs28728162
Chromosome Location	chr12:121968847-121968848
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:121956002..121958678-chr12:121968184..121970506,2	MCF-7	breast:
2	chr12:121968721..121970386-chr12:121980067..121981656,2	MCF-7	breast:
3	chr12:121966142..121973158-chr12:121973289..121976781,9	MCF-7	breast:
4	chr12:121959310..121962414-chr12:121967014..121969071,3	MCF-7	breast:
5	chr12:121905323..121907586-chr12:121967000..121969065,2	MCF-7	breast:
6	chr12:121967275..121968904-chr12:121970760..121973574,2	MCF-7	breast:
7	chr12:121953228..121956338-chr12:121967346..121970306,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000089094	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs28373517	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28379971	0.96[CEU][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28397967	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28451063	0.86[EUR][1000 genomes]
rs28481788	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28520411	0.83[EUR][1000 genomes]
rs28604990	0.89[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs28620502	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28663167	0.89[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs28667673	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28671138	0.85[EUR][1000 genomes]
rs28687122	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28757753	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28758996	0.83[EUR][1000 genomes]
rs4981000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981004	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4981013	0.83[AMR][1000 genomes]
rs4981016	0.96[CEU][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60370741	0.85[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	nsv560457	chr12:121956483-121976176	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer 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	36 gene(s)	inside rSNPs	diseases
3	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28728162	TAOK3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121932000-121974400	Weak transcription	NHEK	skin
2	chr12:121938200-121971000	Weak transcription	Stomach Mucosa	stomach
3	chr12:121938200-121973800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:121938400-121973600	Weak transcription	Psoas Muscle	Psoas
5	chr12:121938800-121970600	Weak transcription	Fetal Brain Male	brain
6	chr12:121947800-121969400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:121947800-121973400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:121948200-121973600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:121950200-121973800	Weak transcription	HSMMtube	muscle
10	chr12:121953400-121970600	Strong transcription	Fetal Intestine Small	intestine
11	chr12:121957400-121973200	Weak transcription	Colon Smooth Muscle	Colon
12	chr12:121957600-121969200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:121959200-121974000	Weak transcription	Aorta	Aorta
14	chr12:121959400-121972800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:121961400-121970600	Weak transcription	Colonic Mucosa	Colon
16	chr12:121963000-121970200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:121963000-121971000	Weak transcription	Brain Angular Gyrus	brain
18	chr12:121963000-121973600	Weak transcription	Brain Substantia Nigra	brain
19	chr12:121966400-121973600	Weak transcription	Esophagus	oesophagus
20	chr12:121967600-121969200	Weak transcription	Fetal Intestine Large	intestine
21	chr12:121967600-121969200	Weak transcription	Hela-S3	cervix
22	chr12:121967800-121969000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:121967800-121969400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:121967800-121970200	Enhancers	Primary T cells fromperipheralblood	blood
25	chr12:121968000-121969400	Enhancers	Primary B cells from peripheral blood	blood
26	chr12:121968000-121969400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr12:121968000-121969600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr12:121968000-121970400	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr12:121968200-121969000	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr12:121968200-121969200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:121968200-121969200	Enhancers	HUVEC	blood vessel
32	chr12:121968200-121969200	Enhancers	NHLF	lung
33	chr12:121968200-121969800	Enhancers	Primary T cells from cord blood	blood
34	chr12:121968200-121970200	Enhancers	Primary B cells from cord blood	blood
35	chr12:121968200-121970600	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr12:121968200-121974600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:121968400-121969000	Enhancers	Muscle Satellite Cultured Cells	--
38	chr12:121968400-121969000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr12:121968400-121969000	Enhancers	Osteobl	bone
40	chr12:121968400-121969200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:121968400-121969200	Enhancers	Primary hematopoietic stem cells	blood
42	chr12:121968400-121969200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr12:121968400-121969200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:121968400-121969400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:121968400-121972400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:121968400-121973000	Genic enhancers	Fetal Thymus	thymus
47	chr12:121968600-121969000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:121968600-121969000	Enhancers	H9 Cell Line	embryonic stem cell
49	chr12:121968600-121969000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
50	chr12:121968600-121969000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links