Variant report

Variant	rs11176060
Chromosome Location	chr12:66541306-66541307
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66536884..66539272-chr12:66539698..66542601,2	MCF-7	breast:
2	chr12:66541034..66542734-chr12:66544918..66547664,2	K562	blood:
3	chr12:66539081..66541895-chr12:66541952..66543781,2	K562	blood:
4	chr12:66523523..66525670-chr12:66539584..66541563,2	MCF-7	breast:
5	chr12:66539518..66541895-chr12:66542239..66543781,2	K562	blood:
6	chr12:66538639..66542023-chr12:66544775..66548196,3	MCF-7	breast:
7	chr12:66538882..66543480-chr12:66561851..66566115,6	MCF-7	breast:

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

Extended variants
information (count: 32 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10400539	0.83[AMR][1000 genomes]
rs10878378	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10878381	0.85[LWK][hapmap];0.84[MKK][hapmap]
rs10878382	0.85[LWK][hapmap];0.86[MKK][hapmap]
rs11176056	0.85[LWK][hapmap];0.86[MKK][hapmap];0.80[AMR][1000 genomes]
rs11176057	0.87[CHD][hapmap]
rs11176063	0.83[AMR][1000 genomes]
rs1168735	0.83[EUR][1000 genomes]
rs1168765	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168766	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168770	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1177578	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1183892	0.89[CEU][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs1184556	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1184884	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1185888	0.89[CEU][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs12823890	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370126	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1436849	0.81[CEU][hapmap];0.93[GIH][hapmap]
rs1898304	0.84[YRI][hapmap]
rs2576187	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2870782	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4296075	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4328252	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7975029	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7979576	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8793	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv526076	chr12:66541306-66546100	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11176060	RP11-745O10.2	cis	lung	GTEx
rs11176060	TMBIM4	cis	normal skin	skin_eQTL
rs11176060	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs11176060	RP11-745O10.2	cis	Esophagus Mucosa	GTEx
rs11176060	RP11-745O10.2	cis	Stomach	GTEx
rs11176060	RP11-745O10.2	cis	Thyroid	GTEx
rs11176060	RP11-745O10.2	cis	Whole Blood	GTEx
rs11176060	RP11-745O10.2	cis	Artery Tibial	GTEx
rs11176060	RP11-745O10.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11176060	TMBIM4	cis	uninvolved skin	skin_eQTL
rs11176060	TMBIM4	cis	lesional skin	skin_eQTL

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	chr12:66527000-66554400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:66530000-66544000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:66530000-66547200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:66532600-66542600	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:66533800-66544000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:66533800-66545000	Weak transcription	Pancreas	Pancrea
12	chr12:66533800-66548000	Weak transcription	Brain Anterior Caudate	brain
13	chr12:66533800-66548400	Weak transcription	Right Atrium	heart
14	chr12:66533800-66553000	Weak transcription	Aorta	Aorta
15	chr12:66533800-66553000	Weak transcription	Spleen	Spleen
16	chr12:66533800-66553800	Weak transcription	Esophagus	oesophagus
17	chr12:66533800-66554400	Weak transcription	Lung	lung
18	chr12:66534000-66547800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:66534600-66541600	Weak transcription	Brain Germinal Matrix	brain
20	chr12:66534600-66544000	Weak transcription	Fetal Stomach	stomach
21	chr12:66534600-66545400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:66534600-66555600	Weak transcription	Small Intestine	intestine
23	chr12:66534800-66541600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:66534800-66552800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:66535000-66542800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:66535800-66545800	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:66535800-66546800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr12:66536200-66541400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr12:66536200-66553600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr12:66536200-66558000	Weak transcription	Fetal Brain Female	brain
31	chr12:66536400-66542600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:66536400-66542800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr12:66536400-66543400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr12:66536400-66543400	Weak transcription	K562	blood
35	chr12:66536400-66547000	Weak transcription	NHLF	lung
36	chr12:66536400-66547200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr12:66536400-66548400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr12:66536400-66549000	Weak transcription	Gastric	stomach
39	chr12:66536400-66552800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr12:66536400-66553000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:66536400-66556200	Weak transcription	Right Ventricle	heart
42	chr12:66536400-66557600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:66536400-66562400	Weak transcription	HMEC	breast
44	chr12:66536600-66547800	Weak transcription	Brain Substantia Nigra	brain
45	chr12:66536800-66546800	Weak transcription	NHDF-Ad	bronchial
46	chr12:66536800-66552800	Weak transcription	HSMMtube	muscle
47	chr12:66536800-66556200	Weak transcription	Left Ventricle	heart
48	chr12:66537000-66541800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr12:66537000-66542600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:66537000-66543800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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