Variant report

Variant	rs56300335
Chromosome Location	chr19:38445132-38445133
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38441551..38443321-chr19:38443505..38445243,2	K562	blood:
2	chr19:38443941..38445562-chr19:38447183..38449175,2	MCF-7	breast:
3	chr19:38438618..38442193-chr19:38444314..38446890,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12150862	0.80[AMR][1000 genomes]
rs12151082	0.80[AMR][1000 genomes]
rs17249138	0.83[AMR][1000 genomes]
rs17249336	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55752822	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55785437	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55813548	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55946812	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55974157	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55983118	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55994045	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56080901	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56184201	0.83[AMR][1000 genomes]
rs56207124	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56230664	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56233644	0.81[AMR][1000 genomes]
rs56246446	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56251160	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56252444	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56676595	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6508755	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7245962	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254248	0.83[EUR][1000 genomes]
rs7257266	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7258011	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73027472	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73027480	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73034922	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73036634	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73036658	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7343065	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8100199	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][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	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	nsv1061106	chr19:38400149-38448723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv544001	chr19:38400149-38448723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs56300335	AC012309.5	cis	Artery Tibial	GTEx
rs56300335	AC012309.5	cis	Esophagus Mucosa	GTEx
rs56300335	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs56300335	AC012309.5	cis	Thyroid	GTEx
rs56300335	AC012309.5	cis	Esophagus Muscularis	GTEx
rs56300335	ZNF781	cis	Thyroid	GTEx
rs56300335	AC012309.5	cis	Heart Left Ventricle	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38425000-38454000	Weak transcription	HSMMtube	muscle
2	chr19:38426600-38448200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr19:38426600-38450800	Weak transcription	Ovary	ovary
4	chr19:38430600-38453600	Weak transcription	Aorta	Aorta
5	chr19:38434000-38447800	Weak transcription	Hela-S3	cervix
6	chr19:38434400-38451800	Weak transcription	Primary T cells from cord blood	blood
7	chr19:38438400-38455600	Enhancers	Primary B cells from peripheral blood	blood
8	chr19:38439000-38445200	Weak transcription	Fetal Heart	heart
9	chr19:38439600-38453000	Weak transcription	Gastric	stomach
10	chr19:38440000-38446400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:38440800-38449600	Enhancers	Primary B cells from cord blood	blood
12	chr19:38441000-38445200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr19:38441000-38446600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr19:38441400-38456800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr19:38441600-38445200	Enhancers	Osteobl	bone
16	chr19:38441600-38449600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr19:38441800-38445600	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr19:38442000-38445600	Enhancers	GM12878-XiMat	blood
19	chr19:38442000-38445800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:38442400-38445200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:38442400-38445400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr19:38442600-38445200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:38442800-38445200	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr19:38443000-38447800	Weak transcription	Stomach Mucosa	stomach
25	chr19:38443200-38445200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr19:38443400-38445200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr19:38443400-38445400	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr19:38443400-38445400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:38443400-38445600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:38443600-38445200	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr19:38443600-38445200	Enhancers	NH-A	brain
32	chr19:38443600-38445800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr19:38443800-38445200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:38443800-38445200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr19:38443800-38445200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr19:38443800-38445200	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr19:38443800-38445400	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr19:38443800-38445400	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr19:38443800-38445400	Enhancers	Fetal Kidney	kidney
40	chr19:38443800-38445600	Enhancers	H1 Cell Line	embryonic stem cell
41	chr19:38443800-38445600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr19:38443800-38445600	Enhancers	Fetal Intestine Large	intestine
43	chr19:38444000-38445200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr19:38444000-38445200	Enhancers	Muscle Satellite Cultured Cells	--
45	chr19:38444000-38445200	Enhancers	Duodenum Mucosa	Duodenum
46	chr19:38444000-38445400	Enhancers	Fetal Intestine Small	intestine
47	chr19:38444000-38446400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr19:38444000-38453200	Weak transcription	Pancreas	Pancrea
49	chr19:38444200-38445200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:38444200-38453800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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