Variant report

Variant	rs2561551
Chromosome Location	chr19:41172145-41172146
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41167496..41181822-chr19:41192475..41200102,20	MCF-7	breast:
2	chr19:41167372..41175149-chr19:41187518..41198541,22	K562	blood:
3	chr19:41166318..41173902-chr19:41219711..41223853,11	K562	blood:
4	chr19:41171985..41176323-chr19:41183438..41185742,3	MCF-7	breast:
5	chr19:41169432..41172402-chr19:41316394..41319342,2	K562	blood:
6	chr19:41171413..41174088-chr19:41312213..41313806,2	MCF-7	breast:
7	chr19:41168092..41172340-chr19:41281558..41285076,7	K562	blood:
8	chr19:41170975..41174075-chr19:41207359..41209061,3	K562	blood:
9	chr19:41169408..41172450-chr19:41308239..41311343,3	MCF-7	breast:
10	chr19:41168879..41172340-chr19:41281648..41285076,4	K562	blood:
11	chr19:41169091..41170622-chr19:41170887..41173199,2	MCF-7	breast:
12	chr19:41171166..41174388-chr19:41302403..41306286,4	K562	blood:
13	chr19:41171645..41173903-chr19:41256454..41259241,2	K562	blood:
14	chr19:41165880..41175149-chr19:41192911..41198858,17	K562	blood:
15	chr19:41171300..41174250-chr19:41255896..41258297,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261857	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000233622	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000086544	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10411347	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2250994	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2561539	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2561542	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2561543	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2561546	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2561547	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2561548	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2561555	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2604860	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2604879	0.80[ASN][1000 genomes]
rs2604892	0.86[AMR][1000 genomes]
rs2604900	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2604904	0.81[ASN][1000 genomes]
rs2604907	0.81[ASN][1000 genomes]
rs4278858	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67971171	0.80[ASN][1000 genomes]
rs7258709	0.81[ASN][1000 genomes]
rs8110611	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	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
5	nsv1064699	chr19:41086506-41174259	Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv870022	chr19:41113071-41178982	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	diseases
9	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
10	nsv2489	chr19:41145034-41182170	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
11	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
rs2561551	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	chr19:41169600-41173000	Weak transcription	Aorta	Aorta
2	chr19:41169600-41173800	Weak transcription	Small Intestine	intestine
3	chr19:41169600-41174000	Weak transcription	Primary T cells from cord blood	blood
4	chr19:41169800-41172600	Weak transcription	Esophagus	oesophagus
5	chr19:41169800-41172800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr19:41169800-41172800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr19:41169800-41172800	Weak transcription	Brain Anterior Caudate	brain
8	chr19:41169800-41172800	Weak transcription	Gastric	stomach
9	chr19:41169800-41173000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:41169800-41173200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr19:41169800-41173400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:41169800-41173600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr19:41169800-41174400	Weak transcription	Brain Angular Gyrus	brain
14	chr19:41169800-41175000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:41169800-41175000	Weak transcription	Brain Substantia Nigra	brain
16	chr19:41169800-41175000	Weak transcription	Fetal Heart	heart
17	chr19:41169800-41175000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr19:41169800-41184000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr19:41169800-41195400	Weak transcription	Psoas Muscle	Psoas
20	chr19:41170000-41172200	Weak transcription	HUVEC	blood vessel
21	chr19:41170000-41172400	Weak transcription	Fetal Brain Female	brain
22	chr19:41170000-41172400	Enhancers	A549	lung
23	chr19:41170000-41172400	Weak transcription	HSMM	muscle
24	chr19:41170000-41172400	Weak transcription	NHDF-Ad	bronchial
25	chr19:41170000-41172600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr19:41170000-41172600	Weak transcription	Right Ventricle	heart
27	chr19:41170000-41172800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr19:41170000-41172800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr19:41170000-41172800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:41170000-41172800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr19:41170000-41172800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:41170000-41172800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr19:41170000-41172800	Weak transcription	Adipose Nuclei	Adipose
34	chr19:41170000-41172800	Weak transcription	Liver	Liver
35	chr19:41170000-41172800	Weak transcription	Colonic Mucosa	Colon
36	chr19:41170000-41172800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr19:41170000-41172800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr19:41170000-41173000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr19:41170000-41173000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:41170000-41173000	Weak transcription	Ovary	ovary
41	chr19:41170000-41173400	Weak transcription	Pancreas	Pancrea
42	chr19:41170000-41173600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:41170000-41173600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr19:41170000-41173800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr19:41170000-41173800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr19:41170000-41174000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:41170000-41174000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:41170000-41174000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr19:41170000-41174000	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr19:41170000-41174000	Weak transcription	Brain Inferior Temporal Lobe	brain

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