Variant report

Variant	rs2578192
Chromosome Location	chr18:43669184-43669185
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:43668214-43669529	GM12878	blood:	n/a	n/a
2	POLR2A	chr18:43668254-43669451	GM12878	blood:	n/a	n/a
3	POLR2A	chr18:43668935-43669404	K562	blood:	n/a	n/a
4	POLR2A	chr18:43668494-43669237	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:43668900..43671493-chr18:43677433..43680075,2	MCF-7	breast:

Variant related genes	Relation type
ATP5A1	TF binding region
ENSG00000152234	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12709735	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12954742	0.88[ASN][1000 genomes]
rs12966247	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1866321	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1964984	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2467669	0.85[ASN][1000 genomes]
rs2515639	0.85[ASN][1000 genomes]
rs2578183	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2578188	0.83[ASN][1000 genomes]
rs2578189	0.85[ASN][1000 genomes]
rs2578190	0.82[ASN][1000 genomes]
rs2578193	0.82[ASN][1000 genomes]
rs2850644	0.85[ASN][1000 genomes]
rs2850646	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852362	0.80[ASN][1000 genomes]
rs2852363	0.81[ASN][1000 genomes]
rs2853801	0.82[ASN][1000 genomes]
rs2853802	0.82[ASN][1000 genomes]
rs28805990	0.82[ASN][1000 genomes]
rs35122885	0.81[ASN][1000 genomes]
rs35935345	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3744992	0.84[ASN][1000 genomes]
rs3745002	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3753069	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4257298	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4275936	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs474878	0.82[ASN][1000 genomes]
rs4890624	0.82[ASN][1000 genomes]
rs59082804	0.80[ASN][1000 genomes]
rs6507664	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71364518	0.82[ASN][1000 genomes]
rs7238347	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7239525	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7244632	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8085773	0.82[ASN][1000 genomes]
rs8096719	0.85[AMR][1000 genomes]
rs9950234	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9955008	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9962297	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9965812	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064882	chr18:43558343-43687674	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543693	chr18:43558343-43687674	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1062024	chr18:43589516-43749410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv543694	chr18:43589516-43749410	Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2578192	C18orf25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43653600-43669600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr18:43657000-43672200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr18:43657200-43669600	Strong transcription	Primary B cells from cord blood	blood
4	chr18:43657200-43673800	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr18:43657200-43674800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr18:43657200-43674800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr18:43657200-43675000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr18:43657200-43675400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr18:43657200-43675400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr18:43657200-43675600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr18:43657200-43676000	Strong transcription	Osteobl	bone
12	chr18:43657200-43676200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr18:43657400-43669400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr18:43657400-43673400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr18:43657400-43674600	Strong transcription	Liver	Liver
16	chr18:43657400-43674800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr18:43657400-43675000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr18:43657400-43675200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr18:43657400-43675400	Strong transcription	Placenta	Placenta
20	chr18:43657400-43675800	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr18:43657400-43675800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr18:43657600-43669400	Strong transcription	Fetal Thymus	thymus
23	chr18:43657600-43672400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr18:43657600-43673400	Strong transcription	Dnd41	blood
25	chr18:43657600-43674400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr18:43657600-43674600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr18:43657600-43675200	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr18:43657800-43675200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr18:43657800-43675800	Strong transcription	Fetal Muscle Leg	muscle
30	chr18:43657800-43676600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr18:43658000-43669200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr18:43658000-43670000	Strong transcription	Fetal Stomach	stomach
33	chr18:43658000-43670600	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr18:43658000-43670800	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr18:43658000-43675400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr18:43658200-43671800	Weak transcription	Right Atrium	heart
37	chr18:43658600-43675000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr18:43658600-43675400	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr18:43658800-43674200	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr18:43658800-43674400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr18:43659000-43674800	Strong transcription	HUVEC	blood vessel
42	chr18:43659000-43675200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr18:43659000-43675200	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr18:43659000-43676000	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr18:43659200-43669200	Strong transcription	A549	lung
46	chr18:43659200-43672000	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr18:43659200-43675000	Strong transcription	Fetal Brain Female	brain
48	chr18:43659200-43675800	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr18:43659400-43671800	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr18:43659400-43675800	Strong transcription	HMEC	breast

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