Variant report

Variant	rs13290446
Chromosome Location	chr9:16672204-16672205
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10962530	0.84[ASW][hapmap];0.82[CEU][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13285378	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[GIH][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13295818	0.85[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13296034	0.89[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13301628	0.87[CEU][hapmap];0.88[AMR][1000 genomes]
rs1411428	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs6475067	1.00[ASW][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.91[MKK][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7046154	1.00[GIH][hapmap]

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	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
6	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
7	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
8	nsv892648	chr9:16661092-16680901	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13290446	DENND4C	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16657600-16681400	Weak transcription	Psoas Muscle	Psoas
2	chr9:16665000-16704400	Weak transcription	Aorta	Aorta
3	chr9:16667200-16681000	Weak transcription	Fetal Stomach	stomach
4	chr9:16668400-16679000	Weak transcription	Ovary	ovary
5	chr9:16668800-16679600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr9:16669000-16681400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:16670200-16675200	Enhancers	NHDF-Ad	bronchial
8	chr9:16670800-16672400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:16670800-16674400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:16671000-16673600	Enhancers	NH-A	brain
11	chr9:16671200-16675200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:16671200-16679600	Weak transcription	HUVEC	blood vessel
13	chr9:16671200-16679800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr9:16671200-16681200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:16671400-16673400	Enhancers	A549	lung
16	chr9:16671600-16672800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:16671600-16679600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:16671800-16678800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:16672000-16672600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:16672000-16673200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:16672000-16673600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:16672000-16674400	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:16672000-16679400	Weak transcription	HSMM	muscle
24	chr9:16672000-16679600	Weak transcription	HSMMtube	muscle
25	chr9:16672000-16680800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:16672000-16681400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:16672200-16672800	Weak transcription	Fetal Kidney	kidney
28	chr9:16672200-16672800	Weak transcription	Osteobl	bone
29	chr9:16672200-16673400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr9:16672200-16673400	Weak transcription	NHLF	lung
31	chr9:16672200-16679000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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