Variant report

Variant	rs4278858
Chromosome Location	chr19:41168606-41168607
allele	C/T
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:34)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:34 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41167967..41170914-chr19:41255476..41260607,5	K562	blood:
2	chr19:41167992..41170856-chr19:41220892..41222830,4	MCF-7	breast:
3	chr19:41035096..41035993-chr19:41168472..41169257,2	K562	blood:
4	chr19:41167496..41181822-chr19:41192475..41200102,20	MCF-7	breast:
5	chr19:41167287..41169951-chr19:41180209..41183939,4	K562	blood:
6	chr19:41167372..41175149-chr19:41187518..41198541,22	K562	blood:
7	chr19:41167522..41169643-chr19:41327340..41330313,2	K562	blood:
8	chr19:41166318..41173902-chr19:41219711..41223853,11	K562	blood:
9	chr19:41167412..41170593-chr19:41311083..41314714,4	K562	blood:
10	chr19:41168344..41169236-chr19:41303602..41304477,3	K562	blood:
11	chr19:41168336..41169802-chr19:41208137..41209143,10	K562	blood:
12	chr19:41167276..41170716-chr19:41255553..41260607,5	K562	blood:
13	chr19:41168465..41169261-chr19:41208526..41209044,2	MCF-7	breast:
14	chr19:41168379..41168947-chr19:41650043..41650891,2	MCF-7	breast:
15	chr19:41167397..41170684-chr19:41303413..41305834,3	K562	blood:
16	chr19:41168190..41170957-chr19:41311771..41313927,2	MCF-7	breast:
17	chr19:41168219..41171584-chr19:41206436..41210632,6	K562	blood:
18	chr19:41167978..41171618-chr19:41220706..41223395,4	K562	blood:
19	chr19:41168297..41169269-chr19:41312417..41313701,5	K562	blood:
20	chr19:41168092..41172340-chr19:41281558..41285076,7	K562	blood:
21	chr19:41168026..41170815-chr19:41206453..41210632,5	K562	blood:
22	chr19:41167265..41169750-chr19:41244881..41246475,2	K562	blood:
23	chr19:41167833..41170600-chr19:41173317..41176394,3	MCF-7	breast:
24	chr19:41168010..41170261-chr19:41227028..41229783,2	MCF-7	breast:
25	chr19:41167063..41169024-chr19:41256743..41258635,2	MCF-7	breast:
26	chr19:41167397..41169122-chr19:41302727..41305544,2	K562	blood:
27	chr19:41166820..41170120-chr19:41221252..41223641,4	MCF-7	breast:
28	chr19:41167604..41169256-chr19:41246232..41247999,2	MCF-7	breast:
29	chr19:41167418..41169032-chr19:41313685..41315602,2	MCF-7	breast:
30	chr19:41165880..41175149-chr19:41192911..41198858,17	K562	blood:
31	chr19:41167374..41169266-chr19:41303175..41305652,3	MCF-7	breast:
32	chr19:41167628..41170437-chr19:41315910..41318446,2	MCF-7	breast:
33	chr19:41161679..41164682-chr19:41165107..41169222,4	K562	blood:
34	chr19:41168390..41169254-chr19:41313514..41314116,2	MCF-7	breast:

No data

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

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10409296	0.87[ASN][1000 genomes]
rs10411059	0.90[ASN][1000 genomes]
rs10411347	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10421223	0.84[ASN][1000 genomes]
rs2250994	0.90[EUR][1000 genomes]
rs2561539	0.86[EUR][1000 genomes]
rs2561542	0.87[EUR][1000 genomes]
rs2561543	0.88[EUR][1000 genomes]
rs2561546	0.88[EUR][1000 genomes]
rs2561547	0.90[EUR][1000 genomes]
rs2561548	0.88[EUR][1000 genomes]
rs2561551	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2561555	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2561562	0.90[ASN][1000 genomes]
rs2604860	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2604861	0.88[ASN][1000 genomes]
rs2604900	0.90[EUR][1000 genomes]
rs2604904	0.93[ASN][1000 genomes]
rs2604907	0.93[ASN][1000 genomes]
rs67971171	0.92[ASN][1000 genomes]
rs7258709	0.93[ASN][1000 genomes]
rs8110611	0.86[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
rs4278858	C19orf54	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41158400-41168800	Weak transcription	Right Atrium	heart
2	chr19:41165600-41168800	Weak transcription	NHDF-Ad	bronchial
3	chr19:41168000-41168800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:41168200-41168800	Enhancers	Primary T cells fromperipheralblood	blood
5	chr19:41168200-41168800	Enhancers	Fetal Intestine Small	intestine
6	chr19:41168200-41168800	Enhancers	Dnd41	blood
7	chr19:41168200-41169000	Enhancers	Placenta	Placenta
8	chr19:41168200-41169400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr19:41168400-41168800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr19:41168400-41168800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr19:41168400-41168800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:41168400-41168800	Enhancers	Primary hematopoietic stem cells	blood
13	chr19:41168400-41168800	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr19:41168400-41168800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:41168400-41168800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr19:41168400-41168800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:41168400-41168800	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr19:41168400-41168800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:41168400-41168800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:41168400-41168800	Enhancers	Liver	Liver
21	chr19:41168400-41168800	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr19:41168400-41168800	Enhancers	Fetal Muscle Trunk	muscle
23	chr19:41168400-41168800	Enhancers	Fetal Muscle Leg	muscle
24	chr19:41168400-41168800	Enhancers	Fetal Stomach	stomach
25	chr19:41168400-41168800	Enhancers	Fetal Thymus	thymus
26	chr19:41168400-41168800	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr19:41168400-41168800	Weak transcription	GM12878-XiMat	blood
28	chr19:41168400-41169400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr19:41168400-41169400	Active TSS	Brain Germinal Matrix	brain
30	chr19:41168400-41169400	Active TSS	Duodenum Mucosa	Duodenum
31	chr19:41168400-41169400	Enhancers	Fetal Brain Male	brain
32	chr19:41168400-41169600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr19:41168400-41170000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr19:41168400-41170000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr19:41168600-41168800	Flanking Active TSS	Primary B cells from peripheral blood	blood
36	chr19:41168600-41168800	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr19:41168600-41168800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr19:41168600-41168800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr19:41168600-41168800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr19:41168600-41168800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr19:41168600-41168800	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr19:41168600-41169000	Active TSS	Primary B cells from cord blood	blood
43	chr19:41168600-41169000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:41168600-41169000	Active TSS	Adipose Nuclei	Adipose
45	chr19:41168600-41169200	Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr19:41168600-41169200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:41168600-41169200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr19:41168600-41169200	Active TSS	Brain Cingulate Gyrus	brain
49	chr19:41168600-41169200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr19:41168600-41169200	Active TSS	Fetal Intestine Large	intestine

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