Variant report

Variant	rs2383079
Chromosome Location	chr9:18569858-18569859
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr9:18569832-18569919	MCF10A-Er-Src	breast:	n/a	n/a
2	TCF12	chr9:18569772-18570370	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr9:18569719-18570412	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr9:18569638-18570415	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
MIR3152	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10511660	0.85[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs12001049	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12004058	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13294657	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13295269	0.90[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13295522	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13295553	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13299349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13300372	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13300518	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1341067	0.86[CEU][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1341069	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1341070	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17209122	0.86[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17228625	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1856895	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2383078	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34253990	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34330935	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34540271	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34587944	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35140301	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35159088	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35568696	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35847846	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35875473	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35885690	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57985853	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58013277	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73425403	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73429674	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7388822	0.86[CEU][hapmap]
rs7389933	0.86[CHB][hapmap]
rs7390343	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7390384	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7465974	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7465987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs951227	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[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	nsv892690	chr9:18485434-18592374	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv428536	chr9:18512807-18667760	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
9	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
10	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
11	nsv892693	chr9:18541710-18584860	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2383079	IFNA16	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18546200-18574000	Weak transcription	Fetal Heart	heart
2	chr9:18564400-18591800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:18566800-18579600	Weak transcription	HSMMtube	muscle
4	chr9:18567000-18573800	Weak transcription	NH-A	brain
5	chr9:18567000-18579600	Weak transcription	HUVEC	blood vessel
6	chr9:18567800-18578000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:18568000-18570000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:18568000-18570600	Enhancers	NHDF-Ad	bronchial
9	chr9:18568400-18570200	Enhancers	Osteobl	bone
10	chr9:18568600-18570800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr9:18569000-18570200	Enhancers	Aorta	Aorta
12	chr9:18569000-18571000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:18569400-18570200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:18569400-18573800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:18569600-18570000	Weak transcription	Fetal Stomach	stomach
16	chr9:18569600-18570200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:18569600-18570600	Strong transcription	HSMM	muscle
18	chr9:18569600-18570600	Enhancers	NHEK	skin
19	chr9:18569600-18575600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr9:18569600-18580200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:18569800-18601000	Weak transcription	NHLF	lung

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