Variant report

Variant	rs28372579
Chromosome Location	chr12:123881176-123881177
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123879767..123882314-chr12:123882742..123884960,2	MCF-7	breast:
2	chr12:123873357..123876856-chr12:123879238..123882589,5	K562	blood:
3	chr12:123880916..123883261-chr12:123885627..123887999,2	K562	blood:

Variant related genes	Relation type
ENSG00000183955	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12299125	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28406193	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28413626	0.89[EUR][1000 genomes]
rs28458312	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28472704	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28481863	0.84[EUR][1000 genomes]
rs28569885	0.82[EUR][1000 genomes]
rs28576953	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28582096	0.92[EUR][1000 genomes]
rs28583837	0.94[EUR][1000 genomes]
rs28592876	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28625019	0.85[EUR][1000 genomes]
rs28636834	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28675824	0.89[EUR][1000 genomes]
rs28676499	0.85[EUR][1000 genomes]
rs28683528	0.87[EUR][1000 genomes]
rs28706696	0.85[EUR][1000 genomes]
rs28715490	0.86[EUR][1000 genomes]
rs28809230	0.91[EUR][1000 genomes]
rs28855757	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4930719	0.85[EUR][1000 genomes]
rs6576	0.82[EUR][1000 genomes]
rs7485502	0.86[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	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv899579	chr12:123843017-123901480	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs28372579	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs28372579	RP11-282O18.3	cis	Adipose Subcutaneous	GTEx
rs28372579	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs28372579	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs28372579	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs28372579	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs28372579	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs28372579	CDK2AP1	cis	Adipose Subcutaneous	GTEx
rs28372579	CDK2AP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123875000-123884400	Strong transcription	Thymus	Thymus
2	chr12:123875000-123886400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:123875200-123884400	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr12:123875200-123884600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:123875200-123894400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:123875400-123882200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:123875400-123882600	Strong transcription	Placenta	Placenta
8	chr12:123875400-123883600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:123875400-123884600	Strong transcription	Primary T cells from cord blood	blood
10	chr12:123875600-123881600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:123875600-123882200	Strong transcription	Colon Smooth Muscle	Colon
12	chr12:123875600-123882800	Weak transcription	Psoas Muscle	Psoas
13	chr12:123875600-123884000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:123875600-123884200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr12:123875600-123884200	Strong transcription	A549	lung
16	chr12:123875600-123884200	Strong transcription	GM12878-XiMat	blood
17	chr12:123875600-123884400	Strong transcription	HMEC	breast
18	chr12:123875600-123884600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:123875600-123885400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:123875600-123894200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:123875600-123895600	Strong transcription	Fetal Thymus	thymus
22	chr12:123875800-123881200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr12:123875800-123881800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr12:123875800-123881800	Strong transcription	NH-A	brain
25	chr12:123875800-123882000	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr12:123875800-123882200	Strong transcription	NHEK	skin
27	chr12:123875800-123884200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr12:123875800-123884600	Strong transcription	Placenta Amnion	Placenta Amnion
29	chr12:123875800-123894000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:123876000-123884400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:123876200-123882800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:123876200-123884400	Strong transcription	Fetal Lung	lung
33	chr12:123876200-123885600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:123876400-123881400	Strong transcription	Fetal Stomach	stomach
35	chr12:123876400-123882600	Strong transcription	Liver	Liver
36	chr12:123876400-123884600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:123876400-123894800	Strong transcription	Fetal Intestine Small	intestine
38	chr12:123876600-123881600	Strong transcription	HSMM	muscle
39	chr12:123876600-123881800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr12:123876600-123881800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr12:123876600-123882000	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:123876600-123882000	Strong transcription	HSMMtube	muscle
43	chr12:123876600-123884000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr12:123876600-123894800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:123876800-123881400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:123876800-123882200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr12:123876800-123882400	Strong transcription	Hela-S3	cervix
48	chr12:123876800-123882600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:123876800-123882800	Strong transcription	Adipose Nuclei	Adipose
50	chr12:123876800-123882800	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links