Variant report

Variant	rs4730985
Chromosome Location	chr7:120665048-120665049
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120662581..120666417-chr7:120714540..120719894,6	K562	blood:
2	chr7:120589944..120591471-chr7:120664683..120667030,2	K562	blood:
3	chr7:120660852..120665277-chr7:120680137..120683898,4	K562	blood:

Variant related genes	Relation type
ENSG00000106034	Chromatin interaction
ENSG00000071243	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10085563	0.83[CEU][hapmap]
rs10229719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10258025	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11363	0.81[EUR][1000 genomes]
rs12672149	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706307	0.83[CEU][hapmap]
rs12706308	0.82[CEU][hapmap]
rs12706309	0.83[CEU][hapmap]
rs12706310	0.83[CEU][hapmap]
rs13881	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs193727	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2013083	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160010	0.83[CEU][hapmap]
rs2215786	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215789	0.83[CEU][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2525711	0.83[CEU][hapmap]
rs2525714	0.83[CEU][hapmap]
rs2525715	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs2525716	0.94[CEU][hapmap]
rs2525717	0.82[CEU][hapmap]
rs2525720	0.83[CEU][hapmap]
rs2525724	0.83[CEU][hapmap]
rs2525725	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs2525726	0.83[CEU][hapmap]
rs2525728	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs2525731	0.85[EUR][1000 genomes]
rs2525732	0.82[EUR][1000 genomes]
rs2525733	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs2525734	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs2525735	0.83[CEU][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2525738	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2525739	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2525740	0.83[CEU][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2538485	0.83[CEU][hapmap]
rs2721326	0.83[CEU][hapmap]
rs2721336	0.83[CEU][hapmap]
rs2721337	0.83[CEU][hapmap]
rs2721340	0.83[CEU][hapmap]
rs2721345	0.83[CEU][hapmap]
rs2721350	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs2721359	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2721361	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2721366	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs2721368	0.83[CEU][hapmap]
rs2721370	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs2896299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3944026	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41691	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41692	0.83[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41693	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41694	0.83[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41695	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41697	0.83[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41698	0.93[ASN][1000 genomes]
rs41703	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41704	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4727915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727917	0.82[CEU][hapmap]
rs4730987	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730988	0.83[CEU][hapmap]
rs6466764	0.83[CEU][hapmap]
rs6953795	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6966297	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6970871	0.83[CEU][hapmap]
rs6973457	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784837	0.83[CEU][hapmap]
rs7789501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808593	0.83[CEU][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
rs4730985	TSPAN12	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120656000-120668000	Weak transcription	Right Atrium	heart
2	chr7:120657800-120666400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr7:120658000-120665600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr7:120660800-120665200	Enhancers	Colon Smooth Muscle	Colon
5	chr7:120661000-120668000	Weak transcription	HSMMtube	muscle
6	chr7:120661600-120669400	Genic enhancers	K562	blood
7	chr7:120662000-120665200	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr7:120662000-120668000	Weak transcription	Fetal Stomach	stomach
9	chr7:120663200-120665200	Enhancers	Fetal Lung	lung
10	chr7:120663200-120666600	Enhancers	NHLF	lung
11	chr7:120663800-120665600	Enhancers	Fetal Kidney	kidney
12	chr7:120663800-120666400	Weak transcription	Left Ventricle	heart
13	chr7:120664000-120665600	Weak transcription	Right Ventricle	heart
14	chr7:120664000-120665800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr7:120664000-120665800	Weak transcription	HSMM	muscle
16	chr7:120664000-120666200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr7:120664000-120668400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr7:120664200-120665200	Active TSS	Stomach Smooth Muscle	stomach
19	chr7:120664200-120666000	Weak transcription	Ovary	ovary
20	chr7:120664400-120665200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr7:120664400-120668200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:120664400-120668400	Weak transcription	Aorta	Aorta
23	chr7:120664600-120665600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:120664600-120666000	Weak transcription	Small Intestine	intestine
25	chr7:120664600-120666200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr7:120664600-120667200	Weak transcription	Fetal Heart	heart
27	chr7:120664600-120667600	Weak transcription	Psoas Muscle	Psoas
28	chr7:120664600-120668000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr7:120664600-120668000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr7:120664600-120668000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr7:120664600-120672800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:120664800-120665400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr7:120665000-120665200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr7:120665000-120665200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr7:120665000-120665200	Flanking Active TSS	Hela-S3	cervix
36	chr7:120665000-120665600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr7:120665000-120666000	Weak transcription	Liver	Liver
38	chr7:120665000-120666000	Enhancers	NHDF-Ad	bronchial
39	chr7:120665000-120666200	Weak transcription	HepG2	liver
40	chr7:120665000-120668000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr7:120665000-120668000	Weak transcription	Adipose Nuclei	Adipose
42	chr7:120665000-120668000	Weak transcription	Osteobl	bone

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