Variant report

Variant	rs73002960
Chromosome Location	chr19:19582992-19582993
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19582961-19583264	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19573739..19577960-chr19:19580596..19583736,3	MCF-7	breast:
2	chr19:19574470..19576025-chr19:19580861..19583746,2	MCF-7	breast:
3	chr19:19580831..19583054-chr19:19584529..19587065,3	K562	blood:

Variant related genes	Relation type
GATAD2A	TF binding region
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10408596	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10408875	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10415849	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11668386	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12052117	0.82[EUR][1000 genomes]
rs28720066	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56241616	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56273306	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56397647	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57009615	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59148799	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8182472	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19577800-19598000	Weak transcription	Ovary	ovary
2	chr19:19578000-19583600	Weak transcription	Pancreas	Pancrea
3	chr19:19579000-19584800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:19579200-19583400	Weak transcription	Esophagus	oesophagus
5	chr19:19579200-19583400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr19:19579200-19583800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:19579200-19585000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr19:19579200-19585000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:19579200-19585400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr19:19579200-19585800	Weak transcription	Hela-S3	cervix
11	chr19:19579200-19586000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:19579200-19598000	Weak transcription	Small Intestine	intestine
13	chr19:19579400-19584000	Weak transcription	Right Ventricle	heart
14	chr19:19579400-19585600	Weak transcription	Fetal Heart	heart
15	chr19:19579400-19599400	Weak transcription	Brain Angular Gyrus	brain
16	chr19:19579600-19583600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr19:19579600-19584800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:19579800-19583200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr19:19579800-19583400	Weak transcription	Colonic Mucosa	Colon
20	chr19:19579800-19583400	Weak transcription	A549	lung
21	chr19:19579800-19583600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:19579800-19583600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:19579800-19583600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr19:19579800-19583600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr19:19579800-19583600	Weak transcription	HMEC	breast
26	chr19:19579800-19583600	Weak transcription	NHLF	lung
27	chr19:19579800-19583800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr19:19579800-19583800	Weak transcription	Brain Hippocampus Middle	brain
29	chr19:19579800-19583800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr19:19579800-19583800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr19:19579800-19585000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr19:19579800-19585000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr19:19579800-19585000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr19:19579800-19585200	Weak transcription	Brain Germinal Matrix	brain
35	chr19:19579800-19585400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr19:19579800-19585400	Weak transcription	NHDF-Ad	bronchial
37	chr19:19579800-19585600	Weak transcription	Fetal Brain Female	brain
38	chr19:19579800-19587400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr19:19579800-19591000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr19:19579800-19593400	Weak transcription	Fetal Kidney	kidney
41	chr19:19579800-19595600	Weak transcription	Osteobl	bone
42	chr19:19579800-19595800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:19579800-19595800	Weak transcription	Colon Smooth Muscle	Colon
44	chr19:19579800-19595800	Weak transcription	HUVEC	blood vessel
45	chr19:19579800-19598600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr19:19579800-19599200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr19:19579800-19599800	Weak transcription	Brain Substantia Nigra	brain
48	chr19:19580000-19583400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr19:19580000-19583800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:19580000-19584800	Weak transcription	Muscle Satellite Cultured Cells	--

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