Variant report

Variant	rs10459263
Chromosome Location	chr12:66538259-66538260
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:66537914..66540757-chr12:66562276..66564016,2	MCF-7	breast:
2	chr12:66537517..66539175-chr12:66547161..66549206,2	MCF-7	breast:
3	chr12:66531775..66535206-chr12:66536994..66539069,3	K562	blood:
4	chr12:66536501..66538595-chr12:66561063..66565036,3	MCF-7	breast:
5	chr12:66537187..66538764-chr12:66565485..66567103,2	K562	blood:
6	chr12:66532321..66535206-chr12:66536994..66538662,2	K562	blood:
7	chr12:66532840..66534600-chr12:66537441..66539657,2	MCF-7	breast:
8	chr12:66523098..66524616-chr12:66537392..66539632,2	MCF-7	breast:
9	chr12:66537078..66538874-chr12:66541977..66543541,2	K562	blood:
10	chr12:66535914..66538687-chr12:66565341..66566985,2	K562	blood:
11	chr12:66536884..66539272-chr12:66539698..66542601,2	MCF-7	breast:

No data

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]
rs10506475	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10506479	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878379	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10878380	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10878384	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878387	0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878388	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176040	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11176041	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11176042	0.90[AFR][1000 genomes];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	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11176047	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11176048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176051	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176058	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]
rs11176059	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168744	0.89[CEU][hapmap];0.87[CHB][hapmap];0.92[GIH][hapmap]
rs1168757	0.92[GIH][hapmap]
rs1168758	0.80[CEU][hapmap];0.96[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs1168771	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs1168772	0.80[CEU][hapmap];0.96[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs1179914	0.89[CEU][hapmap]
rs12230221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230800	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]
rs12306484	0.89[CEU][hapmap];0.92[GIH][hapmap]
rs12423372	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs12426813	0.90[EUR][1000 genomes]
rs12578364	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12578752	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs12578754	0.90[EUR][1000 genomes]
rs12578801	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs12578994	0.89[CEU][hapmap];0.82[CHB][hapmap];0.93[EUR][1000 genomes]
rs12581033	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12581836	0.89[CEU][hapmap];0.88[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];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];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];0.85[YRI][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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12825992	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1370129	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1625441	0.89[CEU][hapmap];0.92[GIH][hapmap]
rs17245364	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1732893	0.89[CEU][hapmap];0.96[GIH][hapmap]
rs17825931	0.81[CHB][hapmap]
rs17825943	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1921080	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1921082	0.89[CEU][hapmap];0.96[GIH][hapmap]
rs2701653	0.92[GIH][hapmap]
rs2870786	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];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	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34552143	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35085853	0.84[EUR][1000 genomes]
rs35131575	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35187440	0.93[EUR][1000 genomes]
rs35447479	1.00[AFR][1000 genomes];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[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57825508	0.87[ASN][1000 genomes]
rs59112451	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60102429	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66767092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71450848	1.00[AFR][1000 genomes];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];0.83[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
rs10459263	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66525400-66562400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:66525600-66549000	Weak transcription	Colonic Mucosa	Colon
3	chr12:66525600-66552400	Weak transcription	Brain Angular Gyrus	brain
4	chr12:66525600-66561800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:66526600-66557200	Weak transcription	Psoas Muscle	Psoas
6	chr12:66526800-66538600	Weak transcription	Hela-S3	cervix
7	chr12:66527000-66554400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:66530000-66540800	Strong transcription	Placenta	Placenta
9	chr12:66530000-66544000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:66530000-66547200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:66532400-66538600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:66532600-66542600	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:66533800-66544000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:66533800-66545000	Weak transcription	Pancreas	Pancrea
15	chr12:66533800-66548000	Weak transcription	Brain Anterior Caudate	brain
16	chr12:66533800-66548400	Weak transcription	Right Atrium	heart
17	chr12:66533800-66553000	Weak transcription	Aorta	Aorta
18	chr12:66533800-66553000	Weak transcription	Spleen	Spleen
19	chr12:66533800-66553800	Weak transcription	Esophagus	oesophagus
20	chr12:66533800-66554400	Weak transcription	Lung	lung
21	chr12:66534000-66547800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:66534600-66541600	Weak transcription	Brain Germinal Matrix	brain
23	chr12:66534600-66544000	Weak transcription	Fetal Stomach	stomach
24	chr12:66534600-66545400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:66534600-66555600	Weak transcription	Small Intestine	intestine
26	chr12:66534800-66538800	Weak transcription	HepG2	liver
27	chr12:66534800-66541600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr12:66534800-66552800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:66535000-66538600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:66535000-66542800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr12:66535200-66541200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr12:66535400-66538600	Strong transcription	Fetal Brain Male	brain
33	chr12:66535800-66545800	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr12:66535800-66546800	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr12:66536000-66538400	Strong transcription	Primary T cells from cord blood	blood
36	chr12:66536000-66539000	Strong transcription	Fetal Intestine Large	intestine
37	chr12:66536000-66539000	Strong transcription	Fetal Thymus	thymus
38	chr12:66536200-66538400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:66536200-66538400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr12:66536200-66538800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:66536200-66538800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:66536200-66541400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr12:66536200-66553600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr12:66536200-66558000	Weak transcription	Fetal Brain Female	brain
45	chr12:66536400-66538400	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:66536400-66538400	Strong transcription	Osteobl	bone
47	chr12:66536400-66538600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr12:66536400-66538600	Strong transcription	Fetal Lung	lung
49	chr12:66536400-66538800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:66536400-66538800	Strong transcription	Adipose Nuclei	Adipose

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