Variant report

Variant	rs2571053
Chromosome Location	chr19:44976058-44976059
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1734622	1.00[ASN][1000 genomes]
rs1865385	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1897821	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1897824	0.97[EUR][1000 genomes]
rs204527	1.00[ASN][1000 genomes]
rs204529	1.00[ASN][1000 genomes]
rs204530	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs204532	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs204542	1.00[ASN][1000 genomes]
rs204548	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs204550	1.00[ASN][1000 genomes]
rs204553	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs204554	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs204556	1.00[ASN][1000 genomes]
rs2117384	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs2461534	0.91[EUR][1000 genomes]
rs2571040	0.91[EUR][1000 genomes]
rs2571041	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571046	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs2571048	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs2571049	0.91[EUR][1000 genomes]
rs2571050	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs2571059	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571116	0.82[EUR][1000 genomes]
rs2686756	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686757	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686758	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs2686762	0.95[EUR][1000 genomes]
rs2686769	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431273	1.00[ASN][1000 genomes]
rs62118145	0.81[EUR][1000 genomes]
rs62118147	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629579	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250221	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8107008	1.00[CHB][hapmap]
rs926020	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs930462	1.00[CHB][hapmap]
rs954314	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912112	chr19:44853707-45011727	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv912114	chr19:44858776-45002563	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1061350	chr19:44869075-45035469	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv524201	chr19:44955927-44978183	ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv525472	chr19:44955927-44978183	ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv912115	chr19:44957508-44995990	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv960853	chr19:44958445-44982821	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv978867	chr19:44963452-44982821	ZNF genes & repeats Strong transcription Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2571053	ZNF180	cis	Muscle Skeletal	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44966800-44992400	ZNF genes & repeats	Liver	Liver
2	chr19:44967200-44992800	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:44969800-44992200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:44971600-44992200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
5	chr19:44972400-44977600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:44972600-44992200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
7	chr19:44975200-44992200	ZNF genes & repeats	Fetal Brain Female	brain
8	chr19:44975400-44992200	ZNF genes & repeats	Brain Hippocampus Middle	brain
9	chr19:44975600-44990000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:44975600-44992200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
11	chr19:44975800-44992200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
12	chr19:44975800-44992200	ZNF genes & repeats	Brain Anterior Caudate	brain
13	chr19:44976000-44992400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links