Variant report

Variant	rs12709735
Chromosome Location	chr18:43687087-43687088
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:43684267..43685785-chr18:43686222..43687771,2	K562	blood:
2	chr18:43673300..43675362-chr18:43687086..43690045,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152234	Chromatin interaction
ENSG00000152240	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12954742	0.91[ASN][1000 genomes]
rs12966247	0.82[ASN][1000 genomes]
rs1866321	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1964984	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2467669	0.83[ASN][1000 genomes]
rs2515639	0.83[ASN][1000 genomes]
rs2578183	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2578188	0.81[ASN][1000 genomes]
rs2578189	0.83[ASN][1000 genomes]
rs2578190	0.80[ASN][1000 genomes]
rs2578192	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2578193	0.80[ASN][1000 genomes]
rs2850644	0.83[ASN][1000 genomes]
rs2850646	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2853801	0.80[ASN][1000 genomes]
rs2853802	0.80[ASN][1000 genomes]
rs28805990	0.80[ASN][1000 genomes]
rs35935345	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3744992	0.83[ASN][1000 genomes]
rs3745002	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3753069	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4257298	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4275936	0.83[ASN][1000 genomes]
rs474878	0.80[ASN][1000 genomes]
rs4890624	0.80[ASN][1000 genomes]
rs59082804	0.82[ASN][1000 genomes]
rs6507664	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71364518	0.81[ASN][1000 genomes]
rs7238347	0.80[ASN][1000 genomes]
rs7239525	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7244632	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8085773	0.80[ASN][1000 genomes]
rs9950234	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9955008	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9962297	0.82[ASN][1000 genomes]
rs9965812	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv962965	chr18:43678008-43706302	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12709735	C18orf25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43685000-43689000	Weak transcription	Gastric	stomach
2	chr18:43685000-43691200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr18:43685000-43693800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr18:43685000-43694400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr18:43685000-43694400	Weak transcription	Esophagus	oesophagus
6	chr18:43685000-43694400	Weak transcription	Left Ventricle	heart
7	chr18:43685000-43707000	Weak transcription	Spleen	Spleen
8	chr18:43685000-43709000	Weak transcription	Pancreas	Pancrea
9	chr18:43685200-43687600	Weak transcription	Fetal Intestine Large	intestine
10	chr18:43685200-43691000	Weak transcription	Right Atrium	heart
11	chr18:43685200-43693800	Weak transcription	Aorta	Aorta
12	chr18:43685200-43696800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr18:43685200-43704200	Weak transcription	Psoas Muscle	Psoas
14	chr18:43685200-43704800	Weak transcription	Placenta	Placenta
15	chr18:43685200-43709000	Weak transcription	Right Ventricle	heart
16	chr18:43685200-43712600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr18:43685200-43712600	Weak transcription	Stomach Mucosa	stomach
18	chr18:43685200-43715200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr18:43685200-43735600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr18:43685400-43687400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr18:43685400-43687400	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr18:43685400-43687400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr18:43685400-43687600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr18:43685400-43687600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr18:43685400-43687600	Weak transcription	K562	blood
26	chr18:43685400-43687800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr18:43685400-43687800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr18:43685400-43687800	Weak transcription	Fetal Intestine Small	intestine
29	chr18:43685400-43688000	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr18:43685400-43688000	Weak transcription	Primary B cells from cord blood	blood
31	chr18:43685400-43688000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr18:43685400-43688000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr18:43685400-43688200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr18:43685400-43688200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr18:43685400-43688400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr18:43685400-43688600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr18:43685400-43688800	Weak transcription	Thymus	Thymus
38	chr18:43685400-43689000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr18:43685400-43689000	Weak transcription	Primary T cells from cord blood	blood
40	chr18:43685400-43689200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr18:43685400-43689200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr18:43685400-43689200	Weak transcription	Liver	Liver
43	chr18:43685400-43689600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr18:43685400-43689800	Weak transcription	Brain Angular Gyrus	brain
45	chr18:43685400-43689800	Weak transcription	Colon Smooth Muscle	Colon
46	chr18:43685400-43690400	Weak transcription	Brain Anterior Caudate	brain
47	chr18:43685400-43693200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr18:43685400-43693200	Weak transcription	Fetal Lung	lung
49	chr18:43685400-43693200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr18:43685400-43693400	Weak transcription	Brain Hippocampus Middle	brain

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