Variant report

Variant	rs7975029
Chromosome Location	chr12:66503798-66503799
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:66501520..66504935-chr12:66522647..66526244,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139233	Chromatin interaction
ENSG00000239335	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10878378	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11176060	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168735	0.85[EUR][1000 genomes]
rs1168765	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168766	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168770	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1177578	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1183892	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1184556	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1184884	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1185888	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs12823890	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1370126	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2576187	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2870782	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4296075	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4328252	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7979576	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs7975029	RP11-745O10.2	cis	Whole Blood	GTEx
rs7975029	RP11-745O10.2	cis	Artery Tibial	GTEx
rs7975029	TMBIM4	cis	lesional skin	skin_eQTL
rs7975029	TMBIM4	cis	normal skin	skin_eQTL
rs7975029	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs7975029	TMBIM4	cis	uninvolved skin	skin_eQTL
rs7975029	RP11-745O10.2	cis	Esophagus Mucosa	GTEx
rs7975029	RP11-745O10.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7975029	RP11-745O10.2	cis	Stomach	GTEx
rs7975029	RP11-745O10.2	cis	Thyroid	GTEx
rs7975029	RP11-745O10.2	cis	lung	GTEx
rs7975029	RP11-745O10.2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:32 , 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	chr12:66501200-66505400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:66501200-66516000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:66501400-66514600	Weak transcription	A549	lung
5	chr12:66501400-66515400	Weak transcription	Liver	Liver
6	chr12:66501600-66505200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr12:66501600-66505400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:66501600-66512200	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:66501600-66513000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:66501600-66513200	Weak transcription	Brain Anterior Caudate	brain
11	chr12:66501600-66513200	Weak transcription	HSMM	muscle
12	chr12:66501600-66513600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:66501600-66513800	Weak transcription	Adipose Nuclei	Adipose
14	chr12:66501600-66514600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:66501600-66514600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:66501600-66514600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:66501600-66516000	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:66501600-66517600	Weak transcription	Right Ventricle	heart
19	chr12:66501800-66512400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr12:66501800-66516800	Weak transcription	NHEK	skin
21	chr12:66502000-66505200	Weak transcription	Osteobl	bone
22	chr12:66502000-66508800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:66502000-66513400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:66502000-66518000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:66502400-66505200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr12:66502400-66515800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:66502400-66516000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr12:66502400-66518400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr12:66502600-66505600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:66502600-66516000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr12:66502600-66516200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:66503400-66505200	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links