Variant report

Variant	rs12230800
Chromosome Location	chr12:66532493-66532494
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66524156..66526872-chr12:66529144..66534313,4	K562	blood:
2	chr12:66530596..66534894-chr12:66562580..66565717,4	K562	blood:
3	chr12:66523095..66527368-chr12:66532414..66535159,4	MCF-7	breast:
4	chr12:66524217..66527472-chr12:66531631..66536698,7	K562	blood:

Variant related genes	Relation type
ENSG00000139233	Chromatin interaction
ENSG00000155957	Chromatin interaction
ENSG00000239335	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10459263	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10506475	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10506479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878379	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10878380	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10878384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878387	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176040	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11176041	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11176042	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176044	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176046	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11176047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11176048	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176050	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176058	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176059	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176061	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176062	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168744	0.82[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap]
rs1168757	0.93[GIH][hapmap]
rs1168758	0.96[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs1168771	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs1168772	0.96[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs1179914	0.88[CEU][hapmap];0.81[CHB][hapmap]
rs12230221	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230240	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12306484	0.88[CEU][hapmap];0.93[GIH][hapmap]
rs12423372	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs12426813	0.90[EUR][1000 genomes]
rs12578364	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12578752	0.82[CEU][hapmap];0.93[EUR][1000 genomes]
rs12578754	0.90[EUR][1000 genomes]
rs12578801	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs12578994	0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes]
rs12581033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12581836	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12582384	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12814331	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12814606	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12821415	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12822410	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12823414	0.85[EUR][1000 genomes]
rs12823732	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12825992	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1370129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1625441	0.88[CEU][hapmap];0.93[GIH][hapmap]
rs17245364	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1732893	0.88[CEU][hapmap];0.96[GIH][hapmap]
rs17825931	0.85[CHB][hapmap]
rs17825943	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1921080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1921082	0.88[CEU][hapmap];0.96[GIH][hapmap]
rs2701653	0.93[GIH][hapmap]
rs2870786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2904498	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34406211	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34552143	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35085853	0.84[EUR][1000 genomes]
rs35131575	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35187440	0.93[EUR][1000 genomes]
rs35447479	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35971570	0.93[EUR][1000 genomes]
rs36073795	0.93[EUR][1000 genomes]
rs4281516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57825508	0.87[ASN][1000 genomes]
rs59112451	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60102429	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66767092	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71450848	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73315943	0.90[EUR][1000 genomes]
rs737614	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[EUR][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	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899214	chr12:66516692-66556960	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12230800	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66525000-66533200	Weak transcription	Gastric	stomach
2	chr12:66525200-66533200	Weak transcription	Esophagus	oesophagus
3	chr12:66525200-66533200	Weak transcription	Pancreas	Pancrea
4	chr12:66525200-66534400	Weak transcription	Small Intestine	intestine
5	chr12:66525400-66533200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr12:66525400-66533200	Weak transcription	Spleen	Spleen
7	chr12:66525400-66533400	Weak transcription	Aorta	Aorta
8	chr12:66525400-66533400	Weak transcription	Fetal Brain Male	brain
9	chr12:66525400-66534400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:66525400-66562400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:66525600-66533200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr12:66525600-66533400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:66525600-66533400	Weak transcription	Brain Substantia Nigra	brain
14	chr12:66525600-66533600	Weak transcription	Right Ventricle	heart
15	chr12:66525600-66536000	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:66525600-66536400	Weak transcription	Stomach Mucosa	stomach
17	chr12:66525600-66549000	Weak transcription	Colonic Mucosa	Colon
18	chr12:66525600-66552400	Weak transcription	Brain Angular Gyrus	brain
19	chr12:66525600-66561800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:66525800-66533400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:66526000-66533400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr12:66526200-66534200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:66526400-66533200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr12:66526400-66536000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr12:66526600-66533200	Weak transcription	Fetal Stomach	stomach
26	chr12:66526600-66533200	Weak transcription	Thymus	Thymus
27	chr12:66526600-66534400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr12:66526600-66534400	Weak transcription	HepG2	liver
29	chr12:66526600-66557200	Weak transcription	Psoas Muscle	Psoas
30	chr12:66526800-66533200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr12:66526800-66533200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:66526800-66538600	Weak transcription	Hela-S3	cervix
33	chr12:66527000-66533200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:66527000-66554400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:66527200-66533200	Weak transcription	Fetal Intestine Small	intestine
36	chr12:66527400-66533200	Weak transcription	Fetal Heart	heart
37	chr12:66529800-66532600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:66529800-66532800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:66529800-66532800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:66529800-66533200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:66529800-66533600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr12:66530000-66532600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:66530000-66532600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:66530000-66532600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:66530000-66532600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:66530000-66532600	Strong transcription	Colon Smooth Muscle	Colon
47	chr12:66530000-66532800	Strong transcription	A549	lung
48	chr12:66530000-66533000	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr12:66530000-66533000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:66530000-66533200	Strong transcription	Primary monocytes fromperipheralblood	blood

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