Variant report

Variant	rs12462485
Chromosome Location	chr19:38316236-38316237
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10422056	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11083438	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083439	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11665877	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11668384	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668434	0.88[AMR][1000 genomes]
rs12610891	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12972712	0.88[AMR][1000 genomes]
rs12981237	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1643470	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1643472	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1725490	0.82[EUR][1000 genomes]
rs17306508	0.88[AMR][1000 genomes]
rs241937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241940	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241941	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241942	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241943	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241944	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241946	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241947	0.96[ASN][1000 genomes]
rs241953	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs241957	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs241959	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241960	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34607899	0.88[AMR][1000 genomes]
rs34949193	0.83[AMR][1000 genomes]
rs35015599	0.88[AMR][1000 genomes]
rs35214625	0.88[AMR][1000 genomes]
rs353405	0.81[EUR][1000 genomes]
rs353406	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs353409	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs353412	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs353413	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36020184	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs36092052	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3752365	0.88[AMR][1000 genomes]
rs3894129	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4482404	0.88[AMR][1000 genomes]
rs4802134	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803536	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803566	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62108355	0.81[AMR][1000 genomes]
rs6508748	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508752	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs697433	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7250668	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254828	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7255551	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8102871	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8103882	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105694	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110417	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8111400	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs856302	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs856309	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1057428	chr19:38282158-38320814	Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1062040	chr19:38294465-38370456	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38309000-38316800	Weak transcription	Stomach Mucosa	stomach
2	chr19:38309600-38319200	ZNF genes & repeats	Fetal Brain Female	brain
3	chr19:38310000-38317000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
4	chr19:38310000-38317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:38310000-38318200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:38310200-38317600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr19:38312000-38317400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
8	chr19:38312000-38317800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
9	chr19:38312000-38317800	ZNF genes & repeats	Ovary	ovary
10	chr19:38312000-38318400	ZNF genes & repeats	Brain Germinal Matrix	brain
11	chr19:38312000-38324000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
12	chr19:38313000-38318800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
13	chr19:38313200-38317800	ZNF genes & repeats	Colon Smooth Muscle	Colon
14	chr19:38314000-38321600	ZNF genes & repeats	Fetal Lung	lung
15	chr19:38314200-38318600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
16	chr19:38314400-38317400	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:38314400-38317800	ZNF genes & repeats	Fetal Muscle Leg	muscle
18	chr19:38314400-38318200	ZNF genes & repeats	Fetal Kidney	kidney
19	chr19:38314400-38319200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
20	chr19:38314400-38324600	ZNF genes & repeats	Adipose Nuclei	Adipose
21	chr19:38314600-38317200	ZNF genes & repeats	Aorta	Aorta
22	chr19:38314600-38317600	ZNF genes & repeats	Fetal Stomach	stomach
23	chr19:38314600-38317600	ZNF genes & repeats	Left Ventricle	heart
24	chr19:38314600-38317800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
25	chr19:38314600-38318200	ZNF genes & repeats	Psoas Muscle	Psoas
26	chr19:38314600-38318400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:38314600-38318600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
28	chr19:38314600-38318600	ZNF genes & repeats	Fetal Brain Male	brain
29	chr19:38314800-38317400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
30	chr19:38315000-38316600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
31	chr19:38315400-38316400	Weak transcription	Brain Angular Gyrus	brain
32	chr19:38315400-38319800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:38315600-38316400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr19:38315600-38317000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
35	chr19:38315800-38316800	Weak transcription	Brain Hippocampus Middle	brain
36	chr19:38315800-38317400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr19:38316000-38316800	Weak transcription	Brain Anterior Caudate	brain

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