Variant report

Variant	rs12150725
Chromosome Location	chr18:9231415-9231416
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12958093	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17413793	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1893198	1.00[ASN][1000 genomes]
rs2155707	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28418978	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34310409	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34452937	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4131992	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4603624	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4797361	0.96[ASN][1000 genomes]
rs4798782	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4798784	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4798786	0.97[ASN][1000 genomes]
rs4798788	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4798791	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56317320	0.81[ASN][1000 genomes]
rs6506649	0.99[ASN][1000 genomes]
rs7228251	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7232337	1.00[ASN][1000 genomes]
rs7506008	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7506291	0.93[ASN][1000 genomes]
rs8089693	0.97[ASN][1000 genomes]
rs8097848	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs894755	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9304033	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9304034	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9304036	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944905	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9946468	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9946475	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9946695	0.96[ASN][1000 genomes]
rs9946852	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9948560	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9959998	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9960129	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv431971	chr18:9081185-9326852	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1055696	chr18:9191679-9309805	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12150725	TWSG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9174600-9233600	Weak transcription	Spleen	Spleen
2	chr18:9174800-9233600	Weak transcription	Pancreas	Pancrea
3	chr18:9184600-9233800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr18:9185200-9233800	Weak transcription	Right Ventricle	heart
5	chr18:9185600-9232400	Weak transcription	Colonic Mucosa	Colon
6	chr18:9188400-9233600	Weak transcription	Esophagus	oesophagus
7	chr18:9188600-9233600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr18:9189200-9233800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr18:9192200-9233600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr18:9192200-9284000	Weak transcription	NHEK	skin
11	chr18:9201000-9232000	Weak transcription	Brain Substantia Nigra	brain
12	chr18:9201200-9232800	Weak transcription	Gastric	stomach
13	chr18:9202200-9234000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr18:9211200-9231600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr18:9211800-9254800	Weak transcription	NH-A	brain
16	chr18:9212200-9254200	Weak transcription	Hela-S3	cervix
17	chr18:9213200-9232200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr18:9214800-9232000	Weak transcription	HSMMtube	muscle
19	chr18:9215200-9232200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr18:9215800-9233800	Weak transcription	Aorta	Aorta
21	chr18:9216000-9250000	Weak transcription	Small Intestine	intestine
22	chr18:9216000-9289600	Weak transcription	HMEC	breast
23	chr18:9216400-9232200	Weak transcription	Psoas Muscle	Psoas
24	chr18:9216400-9232600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr18:9217000-9233800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr18:9218400-9232000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr18:9219000-9232200	Weak transcription	NHLF	lung
28	chr18:9219000-9232400	Weak transcription	Thymus	Thymus
29	chr18:9222400-9232200	Weak transcription	Colon Smooth Muscle	Colon
30	chr18:9222400-9232200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr18:9222400-9232200	Weak transcription	HUVEC	blood vessel
32	chr18:9222400-9232400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr18:9222400-9233600	Weak transcription	Brain Angular Gyrus	brain
34	chr18:9222600-9234000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr18:9222800-9232200	Weak transcription	Brain Anterior Caudate	brain
36	chr18:9222800-9232400	Weak transcription	Fetal Brain Male	brain
37	chr18:9223000-9232400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr18:9223000-9241400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr18:9224400-9240600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr18:9224800-9232200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr18:9225800-9232000	Weak transcription	K562	blood
42	chr18:9226200-9232000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr18:9226400-9232800	Weak transcription	Lung	lung
44	chr18:9226600-9231600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr18:9226600-9233800	Weak transcription	Left Ventricle	heart
46	chr18:9226800-9232000	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr18:9226800-9232200	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr18:9226800-9233800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr18:9226800-9238000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr18:9227000-9232200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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