Variant report

Variant	rs56252444
Chromosome Location	chr19:38467642-38467643
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38463904..38465863-chr19:38467439..38469281,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs17249336	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55752822	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55785437	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55813548	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55946812	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55974157	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55983118	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55994045	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56080901	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56207124	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56230664	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56246446	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56251160	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56300335	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56676595	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6508755	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7245962	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7257266	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7258011	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73034922	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73036634	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73036658	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8100199	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[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	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs56252444	AC012309.5	cis	Artery Tibial	GTEx
rs56252444	ZNF781	cis	Thyroid	GTEx
rs56252444	AC012309.5	cis	Thyroid	GTEx
rs56252444	AC012309.5	cis	Heart Left Ventricle	GTEx
rs56252444	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs56252444	AC012309.5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38457200-38470400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:38457600-38470200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:38457600-38470400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr19:38457600-38470400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr19:38457800-38468200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr19:38457800-38468400	Weak transcription	NH-A	brain
7	chr19:38458200-38468600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:38460600-38468200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:38461000-38468200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:38461200-38468200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr19:38461600-38468200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:38461600-38468400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr19:38461600-38468400	Weak transcription	Osteobl	bone
14	chr19:38461600-38468600	Weak transcription	Pancreas	Pancrea
15	chr19:38461600-38470200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr19:38461600-38470200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr19:38461600-38470200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr19:38461600-38470200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr19:38461600-38470400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:38461600-38470400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:38461600-38470400	Weak transcription	Gastric	stomach
22	chr19:38461600-38472000	Weak transcription	NHDF-Ad	bronchial
23	chr19:38461600-38476600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:38461600-38493600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:38461600-38493600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr19:38461800-38470600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr19:38461800-38476800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr19:38462000-38467800	Weak transcription	Aorta	Aorta
29	chr19:38462000-38470200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr19:38462200-38470800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr19:38462200-38471800	Enhancers	Primary B cells from peripheral blood	blood
32	chr19:38462800-38468000	Weak transcription	Brain Angular Gyrus	brain
33	chr19:38463200-38468800	Weak transcription	Esophagus	oesophagus
34	chr19:38463400-38470400	Weak transcription	Colonic Mucosa	Colon
35	chr19:38463600-38469000	Weak transcription	Fetal Intestine Large	intestine
36	chr19:38463600-38476000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr19:38463800-38468200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:38463800-38468200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr19:38463800-38468200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:38463800-38476200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr19:38463800-38484800	Weak transcription	Fetal Stomach	stomach
42	chr19:38464000-38468200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr19:38464000-38468400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:38464000-38470400	Weak transcription	Fetal Muscle Leg	muscle
45	chr19:38464200-38469800	Strong transcription	Fetal Intestine Small	intestine
46	chr19:38465000-38468200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr19:38465200-38470200	Weak transcription	Liver	Liver
48	chr19:38465400-38468200	Weak transcription	Lung	lung
49	chr19:38465600-38468400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr19:38466000-38470200	Weak transcription	Stomach Mucosa	stomach

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