Variant report

Variant	rs7039706
Chromosome Location	chr9:16645242-16645243
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1003069	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs1003070	0.82[ASN][1000 genomes]
rs1029015	1.00[YRI][hapmap]
rs10810578	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10810581	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs10810583	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1337387	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1337389	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1337390	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1415471	1.00[YRI][hapmap]
rs2050617	0.81[CEU][hapmap]
rs4112791	0.82[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes]
rs4961727	0.96[CEU][hapmap]
rs7034582	0.90[CHB][hapmap]
rs9886876	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv430000	chr9:16603483-16671045	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv2758627	chr9:16641966-16809203	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv2759673	chr9:16641966-16809203	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7039706	SLC24A2	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16629600-16653600	Weak transcription	HUVEC	blood vessel
2	chr9:16636400-16645800	Weak transcription	Ovary	ovary
3	chr9:16637800-16652600	Weak transcription	Fetal Stomach	stomach
4	chr9:16638000-16651200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:16640000-16670800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:16641000-16645800	Weak transcription	HSMMtube	muscle
7	chr9:16641200-16646000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr9:16641200-16649400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:16641400-16651400	Weak transcription	A549	lung
10	chr9:16643000-16645800	Weak transcription	HSMM	muscle
11	chr9:16643000-16651800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:16643200-16646200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:16643200-16646200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:16643200-16651400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:16643200-16652600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:16643200-16652600	Weak transcription	NHLF	lung
17	chr9:16643200-16653400	Weak transcription	NHDF-Ad	bronchial
18	chr9:16643400-16652400	Weak transcription	Osteobl	bone
19	chr9:16643600-16653600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:16644200-16645400	Enhancers	Colon Smooth Muscle	Colon
21	chr9:16644800-16645400	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr9:16644800-16651000	Weak transcription	Fetal Lung	lung
23	chr9:16645000-16645400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:16645000-16646200	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr9:16645000-16648200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:16645000-16652600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr9:16645200-16645600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:16645200-16651400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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