Variant report

Variant	rs12706306
Chromosome Location	chr7:120666769-120666770
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:120589944..120591471-chr7:120664683..120667030,2	K562	blood:
2	chr7:120665801..120667354-chr7:120675569..120677821,2	K562	blood:

Variant related genes	Relation type
ENSG00000071243	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10245811	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs10245939	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10257314	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10277935	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1080807	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10953923	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1118142	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12706305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17535702	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1981711	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2058501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2074577	0.81[YRI][hapmap]
rs2248890	0.82[YRI][hapmap]
rs2525712	0.83[YRI][hapmap]
rs2721354	0.81[YRI][hapmap]
rs6944789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6949989	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6956237	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6958635	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6960415	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7782014	0.82[CHB][hapmap]
rs7782552	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7802665	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831114	chr7:120595624-120804510	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv608327	chr7:120633006-120873078	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv2753621	chr7:120635049-120800049	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1030988	chr7:120636796-120672504	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1023611	chr7:120638930-120881658	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1025430	chr7:120638930-121179289	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv1030792	chr7:120662815-120917533	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12706306	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120656000-120668000	Weak transcription	Right Atrium	heart
2	chr7:120661000-120668000	Weak transcription	HSMMtube	muscle
3	chr7:120661600-120669400	Genic enhancers	K562	blood
4	chr7:120662000-120668000	Weak transcription	Fetal Stomach	stomach
5	chr7:120664000-120668400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:120664400-120668200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:120664400-120668400	Weak transcription	Aorta	Aorta
8	chr7:120664600-120667200	Weak transcription	Fetal Heart	heart
9	chr7:120664600-120667600	Weak transcription	Psoas Muscle	Psoas
10	chr7:120664600-120668000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:120664600-120668000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr7:120664600-120668000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:120664600-120672800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr7:120665000-120668000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:120665000-120668000	Weak transcription	Adipose Nuclei	Adipose
16	chr7:120665000-120668000	Weak transcription	Osteobl	bone
17	chr7:120665200-120668000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:120665200-120668400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:120665200-120672800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr7:120665800-120667800	Strong transcription	HSMM	muscle
21	chr7:120666000-120667000	ZNF genes & repeats	Ovary	ovary
22	chr7:120666200-120667200	Enhancers	HepG2	liver
23	chr7:120666200-120668000	Weak transcription	Colon Smooth Muscle	Colon
24	chr7:120666200-120668000	Weak transcription	Fetal Kidney	kidney
25	chr7:120666400-120668200	Weak transcription	Right Ventricle	heart
26	chr7:120666400-120668600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr7:120666600-120666800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:120666600-120667000	Weak transcription	Left Ventricle	heart
29	chr7:120666600-120667400	Weak transcription	Fetal Lung	lung
30	chr7:120666600-120667600	Weak transcription	NHLF	lung
31	chr7:120666600-120668000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr7:120666600-120668000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr7:120666600-120668000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr7:120666600-120668000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr7:120666600-120668600	Weak transcription	NHDF-Ad	bronchial
36	chr7:120666600-120672800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:120666600-120673000	Weak transcription	Small Intestine	intestine
38	chr7:120666600-120683600	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links