Variant report

Variant	rs530120
Chromosome Location	chr9:18717903-18717904
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10811021	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2779124	0.82[ASN][1000 genomes]
rs479642	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs480335	0.99[ASN][1000 genomes]
rs482009	1.00[ASW][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs484122	0.94[ASN][1000 genomes]
rs502981	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs518607	0.94[CHD][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs521546	0.94[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs521911	0.86[MEX][hapmap]
rs532101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1029449	chr9:18414752-18829127	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv540077	chr9:18414752-18829127	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv1030931	chr9:18414752-18903530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv892691	chr9:18519699-18805483	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv892692	chr9:18519699-19045502	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv831523	chr9:18592398-18753451	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv892694	chr9:18599029-18767830	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
11	nsv892697	chr9:18700566-18767830	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs530120	IFNA13	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18706200-18721200	Weak transcription	Aorta	Aorta
2	chr9:18707200-18720800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:18708000-18722400	Weak transcription	NHLF	lung
4	chr9:18708600-18718400	Weak transcription	Fetal Stomach	stomach
5	chr9:18708600-18726400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:18708800-18721400	Weak transcription	Fetal Lung	lung
7	chr9:18708800-18727000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:18710400-18721400	Weak transcription	NH-A	brain
9	chr9:18710400-18756400	Weak transcription	HSMMtube	muscle
10	chr9:18711000-18722600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:18711200-18719600	Weak transcription	Osteobl	bone
12	chr9:18711200-18720400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr9:18711400-18720400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:18711400-18721000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:18717600-18718000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:18717600-18718000	Enhancers	NHDF-Ad	bronchial
17	chr9:18717600-18721400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr9:18717800-18718000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:18717800-18718400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:18717800-18720400	Strong transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links