Variant report

Variant	rs11671953
Chromosome Location	chr19:38180680-38180681
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1060522	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10853710	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11083429	0.81[EUR][1000 genomes]
rs11083433	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11666172	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11668796	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11673497	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16975299	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17246792	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28431170	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2891657	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34991303	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55871826	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55913702	0.98[EUR][1000 genomes]
rs55950325	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62108305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62108351	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6508739	0.98[EUR][1000 genomes]
rs7249622	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7253081	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7258385	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73037060	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8102818	0.81[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11671953	AC012309.5	cis	Thyroid	GTEx
rs11671953	ZNF573	cis	multi-tissue	Pritchard

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38166600-38182600	Weak transcription	Right Ventricle	heart
2	chr19:38169800-38182200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:38170400-38182200	Weak transcription	Brain Substantia Nigra	brain
4	chr19:38170600-38182200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr19:38170800-38182200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr19:38171400-38182200	Weak transcription	Brain Angular Gyrus	brain
7	chr19:38172800-38182200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:38173600-38182800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr19:38173800-38182200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr19:38173800-38182200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr19:38174600-38182200	Weak transcription	Colon Smooth Muscle	Colon
12	chr19:38175000-38182400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr19:38175200-38182400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:38175800-38182200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr19:38176400-38182200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr19:38176400-38182400	Weak transcription	Aorta	Aorta
17	chr19:38176800-38182200	Weak transcription	Fetal Lung	lung
18	chr19:38177400-38182200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr19:38177400-38182200	Weak transcription	HepG2	liver
20	chr19:38177600-38182200	Weak transcription	Psoas Muscle	Psoas
21	chr19:38177600-38182600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr19:38177600-38182800	Weak transcription	Gastric	stomach
23	chr19:38177800-38182200	Weak transcription	Adipose Nuclei	Adipose
24	chr19:38177800-38182200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr19:38177800-38182400	Weak transcription	Primary T cells from cord blood	blood
26	chr19:38178000-38182400	Weak transcription	Ovary	ovary
27	chr19:38178200-38182200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr19:38178200-38182200	Weak transcription	Brain Anterior Caudate	brain
29	chr19:38178600-38180800	Strong transcription	Left Ventricle	heart
30	chr19:38178600-38182200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr19:38178800-38181000	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr19:38179000-38182200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr19:38179000-38182400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr19:38179400-38180800	Strong transcription	Fetal Stomach	stomach
35	chr19:38179400-38182400	Weak transcription	Fetal Muscle Leg	muscle
36	chr19:38179800-38182000	Weak transcription	Fetal Brain Female	brain
37	chr19:38180000-38180800	Weak transcription	Brain Germinal Matrix	brain
38	chr19:38180000-38182000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr19:38180000-38182200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr19:38180000-38182200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr19:38180400-38180800	Strong transcription	Brain Hippocampus Middle	brain
42	chr19:38180400-38181600	Enhancers	Fetal Brain Male	brain
43	chr19:38180400-38181600	Enhancers	Dnd41	blood
44	chr19:38180600-38180800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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