Variant report

Variant	rs62108354
Chromosome Location	chr19:38225176-38225177
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10153500	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10424047	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11878261	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11879149	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11880056	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11880604	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11883255	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34206817	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34743484	0.88[EUR][1000 genomes]
rs45505797	0.83[EUR][1000 genomes]
rs56075341	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56264690	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56281742	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57504517	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57725815	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57867853	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59966837	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60686304	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62108260	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62108262	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62108289	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62108290	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62108292	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62108293	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62108297	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62108344	0.83[AFR][1000 genomes]
rs62108348	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62108350	0.84[ASN][1000 genomes]
rs62110178	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110185	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110186	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110187	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110188	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62111488	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62111490	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245981	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246147	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7247175	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7247345	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7258992	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7259029	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7259717	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73930999	0.83[EUR][1000 genomes]
rs73932929	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73932955	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8101476	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8101991	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8102189	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8104124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8104747	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8108261	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	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

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38210800-38229400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr19:38211000-38225200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr19:38211000-38225200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr19:38211000-38226400	Weak transcription	Psoas Muscle	Psoas
5	chr19:38211000-38227600	Weak transcription	Brain Hippocampus Middle	brain
6	chr19:38211000-38228400	Weak transcription	Fetal Muscle Leg	muscle
7	chr19:38211000-38228600	Weak transcription	Brain Substantia Nigra	brain
8	chr19:38211000-38229200	Weak transcription	Fetal Kidney	kidney
9	chr19:38211000-38229200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr19:38211000-38229200	Weak transcription	Left Ventricle	heart
11	chr19:38211000-38229400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr19:38211000-38229400	Weak transcription	Brain Germinal Matrix	brain
13	chr19:38211000-38229400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:38211000-38230200	Weak transcription	Hela-S3	cervix
15	chr19:38211200-38225600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr19:38211200-38229200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr19:38211200-38229200	Weak transcription	Fetal Brain Female	brain
18	chr19:38211200-38229200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr19:38218400-38229200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr19:38221200-38241800	ZNF genes & repeats	Liver	Liver
21	chr19:38221800-38225200	Weak transcription	Right Ventricle	heart
22	chr19:38221800-38225800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:38222200-38225400	Weak transcription	Pancreas	Pancrea
24	chr19:38222800-38225200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr19:38223600-38225400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr19:38223800-38227000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:38224000-38229400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:38224200-38225400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr19:38224600-38225600	ZNF genes & repeats	Fetal Stomach	stomach
30	chr19:38224600-38241600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:38224800-38225400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr19:38224800-38225400	Weak transcription	Ovary	ovary
33	chr19:38224800-38229200	Weak transcription	Fetal Lung	lung

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