Variant report

Variant	rs1179917
Chromosome Location	chr12:66514723-66514724
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66512970..66515802-chr12:66525883..66527400,2	MCF-7	breast:
2	chr12:66514117..66516247-chr12:66517268..66518852,2	MCF-7	breast:
3	chr12:66512047..66516114-chr12:66522625..66525849,5	MCF-7	breast:
4	chr12:66512389..66515308-chr12:66562827..66565112,2	K562	blood:

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

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10506480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11465955	0.80[EUR][1000 genomes]
rs1168740	0.82[YRI][hapmap]
rs17767286	0.85[EUR][1000 genomes]
rs17767298	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1821777	0.80[EUR][1000 genomes]
rs1882200	0.81[EUR][1000 genomes]
rs1946750	0.82[YRI][hapmap]
rs2289134	0.81[EUR][1000 genomes]
rs2293657	0.80[EUR][1000 genomes]
rs4762087	0.88[EUR][1000 genomes]
rs4762088	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs56156535	0.88[EUR][1000 genomes]
rs56365678	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61927088	0.89[EUR][1000 genomes]
rs61927090	0.88[EUR][1000 genomes]
rs7302556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7315220	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1179917	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66501200-66516000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:66501400-66515400	Weak transcription	Liver	Liver
3	chr12:66501600-66516000	Weak transcription	Brain Hippocampus Middle	brain
4	chr12:66501600-66517600	Weak transcription	Right Ventricle	heart
5	chr12:66501800-66516800	Weak transcription	NHEK	skin
6	chr12:66502000-66518000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:66502400-66515800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:66502400-66516000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:66502400-66518400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:66502600-66516000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:66502600-66516200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:66505400-66516000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:66505800-66515600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:66506400-66516400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:66508600-66515400	Weak transcription	Fetal Brain Female	brain
16	chr12:66509000-66515200	Weak transcription	Lung	lung
17	chr12:66509000-66518200	Weak transcription	Esophagus	oesophagus
18	chr12:66509000-66519800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:66509000-66523800	Weak transcription	Pancreas	Pancrea
20	chr12:66509200-66515800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr12:66509200-66523600	Weak transcription	Gastric	stomach
22	chr12:66509600-66518000	Weak transcription	Ovary	ovary
23	chr12:66510600-66515800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:66511000-66516000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:66511200-66515600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:66511400-66518200	Weak transcription	Fetal Kidney	kidney
27	chr12:66511600-66516200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:66512000-66516000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr12:66512000-66522200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:66512200-66514800	Weak transcription	HUVEC	blood vessel
31	chr12:66512200-66516000	Weak transcription	Brain Germinal Matrix	brain
32	chr12:66512400-66516000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:66512600-66514800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:66512600-66515400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:66512600-66515600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:66512600-66515800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:66512600-66516000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr12:66512600-66516200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:66512600-66516400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr12:66512600-66518000	Weak transcription	Psoas Muscle	Psoas
41	chr12:66512800-66515000	Genic enhancers	GM12878-XiMat	blood
42	chr12:66512800-66517800	Weak transcription	K562	blood
43	chr12:66513000-66515800	Weak transcription	Hela-S3	cervix
44	chr12:66513200-66514800	Weak transcription	Fetal Intestine Large	intestine
45	chr12:66513200-66516000	Weak transcription	NH-A	brain
46	chr12:66513200-66516200	Weak transcription	Placenta	Placenta
47	chr12:66513200-66516800	Weak transcription	Fetal Stomach	stomach
48	chr12:66513200-66517400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:66513400-66515200	Strong transcription	Primary B cells from cord blood	blood
50	chr12:66513400-66516400	Weak transcription	HSMMtube	muscle

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