Variant report

Variant	rs9962297
Chromosome Location	chr18:43648622-43648623
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:43642172..43644592-chr18:43648279..43650859,2	MCF-7	breast:
2	chr18:43640422..43642180-chr18:43647918..43649817,3	K562	blood:
3	chr18:43618150..43620887-chr18:43645999..43648902,3	K562	blood:
4	chr18:43647683..43650654-chr18:43651658..43653260,2	K562	blood:

Variant related genes	Relation type
ENSG00000152229	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12709735	0.82[ASN][1000 genomes]
rs12966247	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1964984	0.80[ASN][1000 genomes]
rs2578192	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2850646	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28524126	0.84[ASN][1000 genomes]
rs35935345	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3745002	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3753069	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4257298	0.80[ASN][1000 genomes]
rs4890311	0.84[EUR][1000 genomes]
rs4890312	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6507663	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7238347	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7239525	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8096719	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9950234	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9952157	0.80[ASN][1000 genomes]
rs9954534	0.84[ASN][1000 genomes]
rs9955008	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9958257	0.82[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
rs9962297	C18orf25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43608600-43651000	Weak transcription	Esophagus	oesophagus
2	chr18:43632400-43651200	Weak transcription	Pancreas	Pancrea
3	chr18:43633200-43651200	Weak transcription	HSMMtube	muscle
4	chr18:43633400-43650200	Weak transcription	NHLF	lung
5	chr18:43636400-43649200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr18:43636400-43650200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr18:43636600-43649600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr18:43637000-43650000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr18:43640800-43650400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr18:43641000-43648800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr18:43641000-43650000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr18:43641000-43650800	Weak transcription	Fetal Intestine Small	intestine
13	chr18:43641400-43648800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr18:43641600-43649000	Weak transcription	Left Ventricle	heart
15	chr18:43642200-43651000	Weak transcription	Gastric	stomach
16	chr18:43642400-43651200	Weak transcription	Lung	lung
17	chr18:43644200-43648800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr18:43644200-43649400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr18:43644800-43650000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr18:43645000-43648800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr18:43645000-43649000	Weak transcription	Placenta	Placenta
22	chr18:43645000-43650000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr18:43645200-43650800	Weak transcription	Osteobl	bone
24	chr18:43646200-43650800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr18:43646800-43648800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr18:43646800-43648800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr18:43646800-43650800	Weak transcription	Spleen	Spleen
28	chr18:43647000-43649000	Weak transcription	Fetal Intestine Large	intestine
29	chr18:43647600-43649000	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr18:43647600-43651000	Weak transcription	Primary T cells from cord blood	blood
31	chr18:43647800-43648800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr18:43647800-43648800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr18:43647800-43648800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr18:43647800-43648800	Weak transcription	GM12878-XiMat	blood
35	chr18:43647800-43650800	Weak transcription	Colon Smooth Muscle	Colon
36	chr18:43648000-43648800	Weak transcription	K562	blood
37	chr18:43648000-43650800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr18:43648000-43651600	Weak transcription	Hela-S3	cervix
39	chr18:43648400-43651000	Enhancers	Liver	Liver
40	chr18:43648600-43648800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr18:43648600-43649000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr18:43648600-43649000	Enhancers	HMEC	breast
43	chr18:43648600-43649000	Enhancers	NHEK	skin
44	chr18:43648600-43649200	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr18:43648600-43649200	Enhancers	Adipose Nuclei	Adipose
46	chr18:43648600-43649800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr18:43648600-43651000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links