Variant report

Variant	rs56271210
Chromosome Location	chr12:66554776-66554777
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	chr12:66550852..66561080-chr12:66561565..66565303,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155957	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10400539	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10506478	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10878381	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10878382	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10878383	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10878389	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10878391	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11176043	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176054	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11176056	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11176063	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11176065	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11176067	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11176068	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11176080	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11176082	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12227630	0.84[EUR][1000 genomes]
rs12832926	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17767200	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1882201	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1898304	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1921083	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2141709	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2178486	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2870781	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34645929	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34755483	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4474482	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4575321	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61927092	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7295147	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7302893	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7305938	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7966453	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7966561	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7979029	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7979775	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv541516	chr12:66547969-66596036	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv976636	chr12:66553474-66556236	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs56271210	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs56271210	RP11-745O10.2	cis	Thyroid	GTEx
rs56271210	RP11-745O10.2	cis	Artery Tibial	GTEx
rs56271210	RP11-745O10.2	cis	Whole Blood	GTEx
rs56271210	RP11-745O10.2	cis	lung	GTEx
rs56271210	RP11-745O10.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:113 , 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	chr12:66525600-66561800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:66526600-66557200	Weak transcription	Psoas Muscle	Psoas
4	chr12:66534600-66555600	Weak transcription	Small Intestine	intestine
5	chr12:66536200-66558000	Weak transcription	Fetal Brain Female	brain
6	chr12:66536400-66556200	Weak transcription	Right Ventricle	heart
7	chr12:66536400-66557600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:66536400-66562400	Weak transcription	HMEC	breast
9	chr12:66536800-66556200	Weak transcription	Left Ventricle	heart
10	chr12:66537400-66556200	Weak transcription	Ovary	ovary
11	chr12:66538400-66556200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:66538600-66560400	Weak transcription	Fetal Brain Male	brain
13	chr12:66539200-66558400	Weak transcription	A549	lung
14	chr12:66539400-66556200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:66539400-66561400	Weak transcription	Fetal Heart	heart
16	chr12:66539400-66562200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr12:66542800-66563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:66544200-66557600	Weak transcription	K562	blood
19	chr12:66545400-66555000	Weak transcription	GM12878-XiMat	blood
20	chr12:66547400-66562000	Weak transcription	HUVEC	blood vessel
21	chr12:66548400-66562200	Weak transcription	Brain Anterior Caudate	brain
22	chr12:66548600-66562000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:66549200-66561800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr12:66549200-66561800	Weak transcription	Right Atrium	heart
25	chr12:66550000-66557600	Strong transcription	Primary T cells from cord blood	blood
26	chr12:66550200-66557400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:66550400-66559200	Weak transcription	Colonic Mucosa	Colon
28	chr12:66550600-66555000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:66551200-66560400	Weak transcription	HepG2	liver
30	chr12:66551400-66558000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr12:66552200-66556000	Strong transcription	Dnd41	blood
32	chr12:66552400-66555000	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr12:66552400-66555400	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr12:66552600-66554800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:66552600-66555600	Strong transcription	Primary B cells from cord blood	blood
36	chr12:66552600-66556000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:66552800-66555000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:66552800-66555000	Strong transcription	Fetal Thymus	thymus
39	chr12:66552800-66555200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:66552800-66555200	Strong transcription	Fetal Muscle Trunk	muscle
41	chr12:66553000-66554800	Strong transcription	Placenta	Placenta
42	chr12:66553000-66555000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:66553000-66555200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:66553000-66555200	Strong transcription	Fetal Stomach	stomach
45	chr12:66553000-66555800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr12:66553000-66555800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:66553000-66562200	Weak transcription	Brain Angular Gyrus	brain
48	chr12:66553200-66555000	Strong transcription	Spleen	Spleen
49	chr12:66553200-66555600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:66553200-66556200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links