Variant report

Variant	rs1882201
Chromosome Location	chr12:66501409-66501410
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	chr12:65694412..65695135-chr12:66501162..66501784,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10400539	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10506478	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10735933	0.81[CHB][hapmap]
rs10878381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878383	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878389	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10878391	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11176043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176054	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11176056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11176063	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11176065	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11176067	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11176068	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11176080	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11176081	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs11176082	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12227630	0.84[EUR][1000 genomes]
rs12832926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17767200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1898304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1921083	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2141709	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2178486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2870781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34645929	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34755483	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4474482	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4575321	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56271210	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61927092	0.83[ASN][1000 genomes]
rs7295147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302893	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305938	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966453	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7966561	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7979029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7979775	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[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	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	nsv832446	chr12:66393863-66501484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1882201	TMBIM4	cis	normal skin	skin_eQTL
rs1882201	RP11-745O10.2	cis	Whole Blood	GTEx
rs1882201	TMBIM4	cis	uninvolved skin	skin_eQTL
rs1882201	RP11-745O10.2	cis	lung	GTEx
rs1882201	TMBIM4	cis	lesional skin	skin_eQTL
rs1882201	RP11-745O10.2	cis	Artery Tibial	GTEx
rs1882201	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs1882201	RP11-745O10.2	cis	Skin Sun Exposed Lower leg	GTEx
rs1882201	RP11-745O10.2	cis	Thyroid	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66500600-66503800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:66500800-66501600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:66500800-66501600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:66500800-66502000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:66501000-66501600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr12:66501000-66501600	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr12:66501000-66501600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:66501000-66501600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:66501000-66501600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:66501000-66501600	Enhancers	Adipose Nuclei	Adipose
11	chr12:66501000-66501600	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr12:66501000-66501600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr12:66501000-66501600	Enhancers	HSMM	muscle
14	chr12:66501000-66501600	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr12:66501000-66501800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:66501000-66501800	Enhancers	NHEK	skin
17	chr12:66501000-66502400	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr12:66501000-66502400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr12:66501000-66502400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr12:66501000-66502600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr12:66501000-66502600	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr12:66501000-66503000	Enhancers	Fetal Brain Male	brain
23	chr12:66501000-66503400	Enhancers	NHDF-Ad	bronchial
24	chr12:66501200-66501600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr12:66501200-66501600	Enhancers	Brain Anterior Caudate	brain
26	chr12:66501200-66501600	Enhancers	Brain Hippocampus Middle	brain
27	chr12:66501200-66501600	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr12:66501200-66501600	Flanking Active TSS	HepG2	liver
29	chr12:66501200-66501800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr12:66501200-66502600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr12:66501200-66505400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:66501200-66516000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr12:66501400-66501600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:66501400-66501600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:66501400-66501600	Enhancers	Right Ventricle	heart
36	chr12:66501400-66501600	Flanking Active TSS	Osteobl	bone
37	chr12:66501400-66502000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr12:66501400-66502000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr12:66501400-66502600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:66501400-66502800	Enhancers	H9 Cell Line	embryonic stem cell
41	chr12:66501400-66514600	Weak transcription	A549	lung
42	chr12:66501400-66515400	Weak transcription	Liver	Liver

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