Variant report

Variant	rs2561546
Chromosome Location	chr19:41184848-41184849
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41183990..41185870-chr19:41193929..41195725,2	K562	blood:
2	chr19:41171985..41176323-chr19:41183438..41185742,3	MCF-7	breast:
3	chr19:41183817..41185577-chr19:41186884..41188446,2	K562	blood:

Variant related genes	Relation type
ENSG00000105245	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10411347	0.92[EUR][1000 genomes]
rs2250994	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2561539	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2561542	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2561543	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2561547	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2561548	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2561549	0.94[ASN][1000 genomes]
rs2561551	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2561555	0.92[EUR][1000 genomes]
rs2604860	0.92[EUR][1000 genomes]
rs2604892	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2604900	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4278858	0.88[EUR][1000 genomes]
rs8110611	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv1058707	chr19:41146147-41200820	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2561546	C19orf54	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41169800-41195400	Weak transcription	Psoas Muscle	Psoas
2	chr19:41172000-41193000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr19:41172400-41191000	Strong transcription	Stomach Smooth Muscle	stomach
4	chr19:41172600-41193400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:41172600-41193600	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr19:41172800-41191000	Strong transcription	Fetal Muscle Trunk	muscle
7	chr19:41172800-41192000	Strong transcription	Duodenum Smooth Muscle	Duodenum
8	chr19:41172800-41192800	Strong transcription	Adipose Nuclei	Adipose
9	chr19:41172800-41193200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:41172800-41193200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr19:41173000-41185200	Strong transcription	Aorta	Aorta
12	chr19:41173000-41192800	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr19:41173000-41192800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:41173000-41192800	Strong transcription	Ovary	ovary
15	chr19:41173000-41193200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr19:41173000-41193200	Strong transcription	Osteobl	bone
17	chr19:41173200-41187200	Strong transcription	Fetal Intestine Large	intestine
18	chr19:41173200-41189800	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr19:41173200-41192600	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr19:41173200-41192800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr19:41173200-41193200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:41173600-41185400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:41173800-41189600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr19:41174000-41185600	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr19:41174000-41187400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr19:41174000-41189600	Strong transcription	HSMM	muscle
27	chr19:41174200-41193200	Strong transcription	Colon Smooth Muscle	Colon
28	chr19:41174400-41185200	Strong transcription	Brain Angular Gyrus	brain
29	chr19:41174800-41190000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr19:41175800-41185000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr19:41175800-41187400	Strong transcription	NH-A	brain
32	chr19:41175800-41190000	Strong transcription	Brain Anterior Caudate	brain
33	chr19:41175800-41192600	Strong transcription	Fetal Muscle Leg	muscle
34	chr19:41175800-41192800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:41175800-41194200	Weak transcription	Fetal Heart	heart
36	chr19:41175800-41196000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr19:41176000-41192800	Weak transcription	GM12878-XiMat	blood
38	chr19:41176000-41195200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr19:41176200-41193200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:41176200-41193200	Strong transcription	Fetal Intestine Small	intestine
41	chr19:41176200-41195600	Weak transcription	Small Intestine	intestine
42	chr19:41176400-41190000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr19:41176400-41192200	Strong transcription	Fetal Brain Female	brain
44	chr19:41176600-41193200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr19:41176800-41193000	Strong transcription	Fetal Stomach	stomach
46	chr19:41176800-41193200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr19:41176800-41193200	Strong transcription	Brain Germinal Matrix	brain
48	chr19:41178200-41185200	Strong transcription	Left Ventricle	heart
49	chr19:41178800-41193200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr19:41179000-41186600	Weak transcription	Primary hematopoietic stem cells	blood

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