Variant report

Variant	rs2028031
Chromosome Location	chr9:104173843-104173844
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:104173472..104176121-chr9:104187429..104190280,2	MCF-7	breast:
2	chr9:104153060..104154833-chr9:104173382..104175911,2	MCF-7	breast:
3	chr9:104165233..104170505-chr9:104171045..104175682,8	MCF-7	breast:
4	chr9:104171442..104174138-chr9:104174646..104177184,3	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1047968	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1047971	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10491511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10512281	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1534828	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17185855	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17186534	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17186716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17186905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17186933	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17766676	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772272	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772308	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772331	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772355	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772612	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772672	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772869	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17773040	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17773076	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1929488	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1929489	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1929491	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2734469	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41296049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41308902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs954738	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2028031	ZNF189	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104163200-104174000	ZNF genes & repeats	Fetal Lung	lung
2	chr9:104163400-104174000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:104164800-104174200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:104164800-104174200	ZNF genes & repeats	Brain Hippocampus Middle	brain
5	chr9:104164800-104175400	ZNF genes & repeats	Fetal Muscle Leg	muscle
6	chr9:104165400-104176200	ZNF genes & repeats	Adipose Nuclei	Adipose
7	chr9:104165600-104178200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
8	chr9:104167000-104174000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
9	chr9:104172000-104176000	Weak transcription	Aorta	Aorta
10	chr9:104172000-104177800	Weak transcription	Lung	lung
11	chr9:104172000-104179200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr9:104172000-104179400	Weak transcription	Pancreas	Pancrea
13	chr9:104172000-104180800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:104172800-104175000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:104172800-104175200	Weak transcription	Fetal Brain Male	brain
16	chr9:104172800-104180800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:104172800-104181200	Weak transcription	Fetal Heart	heart
18	chr9:104172800-104187000	Weak transcription	Left Ventricle	heart
19	chr9:104173600-104175200	Weak transcription	Ovary	ovary
20	chr9:104173600-104175400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:104173600-104177600	Weak transcription	HepG2	liver
22	chr9:104173600-104180400	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links