Variant report

Variant	rs55718806
Chromosome Location	chr19:38106865-38106866
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10445548	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048505	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1061753	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061756	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151156	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17244713	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244769	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17303902	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17304703	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305193	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305228	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305823	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17306900	0.86[ASN][1000 genomes]
rs1871196	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291001	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306201	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385005	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35153242	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55681348	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55743020	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55754546	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55865869	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55909413	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56277404	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56351266	0.86[ASN][1000 genomes]
rs57654288	0.98[EUR][1000 genomes]
rs57943942	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62108291	0.83[EUR][1000 genomes]
rs62108306	0.81[EUR][1000 genomes]
rs7245855	0.86[ASN][1000 genomes]
rs7259272	0.81[EUR][1000 genomes]
rs73031330	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033122	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033134	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033142	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73035159	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73035160	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73039029	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73041006	0.86[ASN][1000 genomes]
rs8101610	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104282	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104994	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108268	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111790	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs55718806	AC012309.5	cis	Esophagus Muscularis	GTEx
rs55718806	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs55718806	ZNF781	cis	Thyroid	GTEx
rs55718806	AC012309.5	cis	Heart Left Ventricle	GTEx
rs55718806	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx
rs55718806	AC012309.5	cis	Thyroid	GTEx
rs55718806	AC012309.5	cis	Artery Tibial	GTEx
rs55718806	AC012309.5	cis	Esophagus Mucosa	GTEx
rs55718806	AC012309.5	cis	Muscle Skeletal	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38087800-38107400	ZNF genes & repeats	Liver	Liver
2	chr19:38089200-38107200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
3	chr19:38095400-38107200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr19:38098200-38107200	ZNF genes & repeats	Adipose Nuclei	Adipose
5	chr19:38105000-38107400	Weak transcription	Brain Angular Gyrus	brain
6	chr19:38105000-38112600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr19:38105000-38116000	Weak transcription	Right Ventricle	heart
8	chr19:38105200-38115000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr19:38105400-38108000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:38106200-38107800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
11	chr19:38106600-38109000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr19:38106800-38107000	ZNF genes & repeats	Brain Hippocampus Middle	brain

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