Variant report

Variant	rs3944026
Chromosome Location	chr7:120664574-120664575
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Variant related genes	Relation type
ENSG00000106034	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10229719	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10258025	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11363	0.86[EUR][1000 genomes]
rs12672149	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13881	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs193727	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2013083	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013087	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074576	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2074577	0.84[CEU][hapmap]
rs2215786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215789	1.00[CEU][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2244863	0.84[CEU][hapmap]
rs2244865	0.85[CEU][hapmap]
rs2525711	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525712	0.85[CEU][hapmap]
rs2525713	0.85[CEU][hapmap]
rs2525714	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525715	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2525716	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525717	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525718	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525719	0.89[CEU][hapmap]
rs2525720	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525722	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525723	0.85[EUR][1000 genomes]
rs2525724	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525725	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2525726	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525728	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2525731	0.90[EUR][1000 genomes]
rs2525732	0.88[EUR][1000 genomes]
rs2525733	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2525734	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2525735	1.00[CEU][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2525738	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2525739	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2525740	1.00[CEU][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2721350	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2721351	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2721359	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2721361	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2721366	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2721368	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2721370	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2721372	0.89[CEU][hapmap]
rs2896299	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41688	0.84[CEU][hapmap]
rs41691	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41692	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41693	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41694	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41695	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41697	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41698	0.93[ASN][1000 genomes]
rs41703	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41704	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4727915	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]
rs4730985	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]
rs4730987	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953795	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6966297	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6973457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7789501	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808535	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

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
rs3944026	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:46 , 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	chr7:120660800-120665000	Enhancers	Liver	Liver
5	chr7:120660800-120665200	Enhancers	Colon Smooth Muscle	Colon
6	chr7:120661000-120668000	Weak transcription	HSMMtube	muscle
7	chr7:120661600-120669400	Genic enhancers	K562	blood
8	chr7:120662000-120665200	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr7:120662000-120668000	Weak transcription	Fetal Stomach	stomach
10	chr7:120662800-120664600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:120663000-120664600	Enhancers	Fetal Heart	heart
12	chr7:120663200-120665000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr7:120663200-120665200	Enhancers	Fetal Lung	lung
14	chr7:120663200-120666600	Enhancers	NHLF	lung
15	chr7:120663400-120664600	Enhancers	Muscle Satellite Cultured Cells	--
16	chr7:120663400-120665000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:120663400-120665000	Enhancers	HepG2	liver
18	chr7:120663600-120664600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr7:120663600-120664600	Enhancers	Psoas Muscle	Psoas
20	chr7:120663600-120664600	Flanking Active TSS	Hela-S3	cervix
21	chr7:120663600-120664600	Enhancers	HUVEC	blood vessel
22	chr7:120663600-120664600	Flanking Active TSS	NHDF-Ad	bronchial
23	chr7:120663600-120664600	Enhancers	Osteobl	bone
24	chr7:120663600-120665000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr7:120663800-120664600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:120663800-120665600	Enhancers	Fetal Kidney	kidney
27	chr7:120663800-120666400	Weak transcription	Left Ventricle	heart
28	chr7:120664000-120664600	Enhancers	NH-A	brain
29	chr7:120664000-120665600	Weak transcription	Right Ventricle	heart
30	chr7:120664000-120665800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr7:120664000-120665800	Weak transcription	HSMM	muscle
32	chr7:120664000-120666200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr7:120664000-120668400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr7:120664200-120664600	Enhancers	Rectal Smooth Muscle	rectum
35	chr7:120664200-120664800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr7:120664200-120664800	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr7:120664200-120665000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr7:120664200-120665000	Enhancers	Adipose Nuclei	Adipose
39	chr7:120664200-120665200	Active TSS	Stomach Smooth Muscle	stomach
40	chr7:120664200-120666000	Weak transcription	Ovary	ovary
41	chr7:120664400-120664600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr7:120664400-120664600	Enhancers	Small Intestine	intestine
43	chr7:120664400-120665000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr7:120664400-120665200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr7:120664400-120668200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr7:120664400-120668400	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links