Variant report

Variant	rs17772869
Chromosome Location	chr9:104183885-104183886
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF189-2	chr9:104181299-104185086	NONHSAT133730

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10123064	1.00[AFR][1000 genomes]
rs1047968	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1047971	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10491511	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10512281	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10989500	1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs10989508	1.00[AFR][1000 genomes]
rs10989509	1.00[AFR][1000 genomes]
rs10989510	1.00[AFR][1000 genomes]
rs10989511	1.00[AFR][1000 genomes]
rs10989514	1.00[AFR][1000 genomes]
rs10989517	1.00[AFR][1000 genomes]
rs12337537	1.00[AFR][1000 genomes]
rs13283255	1.00[AFR][1000 genomes]
rs13289803	1.00[AFR][1000 genomes]
rs13291205	1.00[AFR][1000 genomes]
rs13292387	1.00[AFR][1000 genomes]
rs13293022	1.00[AFR][1000 genomes]
rs13297805	1.00[AFR][1000 genomes]
rs1534828	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17185855	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17186534	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17186716	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17186905	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17186933	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17766676	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772272	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772308	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772331	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772355	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772514	1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs17772612	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772672	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772839	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772845	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17773040	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17773076	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1929488	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1929489	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1929491	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1929492	1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs2028031	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2734469	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34664558	1.00[AFR][1000 genomes]
rs35772088	1.00[AFR][1000 genomes]
rs41296049	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41308902	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41310087	1.00[AFR][1000 genomes]
rs45455902	1.00[AFR][1000 genomes]
rs71491792	1.00[AFR][1000 genomes]
rs954738	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17772869	ZNF189	Cis_1M	lymphoblastoid	RTeQTL
rs17772869	ALDOB	cis	lymphoblastoid	seeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104172800-104187000	Weak transcription	Left Ventricle	heart
2	chr9:104176400-104185600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:104178200-104186800	Weak transcription	Fetal Brain Female	brain
4	chr9:104178400-104187000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:104179400-104188800	Enhancers	HepG2	liver
6	chr9:104180400-104184600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:104180600-104185800	Weak transcription	Brain Hippocampus Middle	brain
8	chr9:104181200-104184000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:104181800-104184000	Weak transcription	Pancreas	Pancrea
10	chr9:104181800-104184200	Weak transcription	HSMMtube	muscle
11	chr9:104181800-104187600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr9:104182400-104189600	Weak transcription	Ovary	ovary
13	chr9:104182600-104184000	Strong transcription	Liver	Liver
14	chr9:104182800-104184600	Strong transcription	Duodenum Mucosa	Duodenum
15	chr9:104183600-104184200	ZNF genes & repeats	Aorta	Aorta
16	chr9:104183600-104184800	Enhancers	Fetal Intestine Large	intestine
17	chr9:104183600-104185000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr9:104183800-104184000	Enhancers	Fetal Lung	lung
19	chr9:104183800-104184400	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links