Variant report

Variant	rs10962530
Chromosome Location	chr9:16667568-16667569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13284907	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13285301	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13285378	0.84[ASW][hapmap];0.86[GIH][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes]
rs13290446	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]
rs13295818	0.95[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13296034	0.95[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs6475067	0.84[ASW][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.91[AMR][1000 genomes]
rs7046154	0.85[CEU][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	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
rs10962530	DENND4C	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16640000-16670800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:16654400-16669200	Weak transcription	NHLF	lung
3	chr9:16656600-16670800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:16657600-16670800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr9:16657600-16670800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:16657600-16671000	Weak transcription	NH-A	brain
7	chr9:16657600-16681400	Weak transcription	Psoas Muscle	Psoas
8	chr9:16659800-16670800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:16661600-16668000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:16662400-16671000	Weak transcription	HSMM	muscle
11	chr9:16663400-16671000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr9:16664400-16668800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:16664400-16671400	Weak transcription	A549	lung
14	chr9:16665000-16667800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:16665000-16668400	Weak transcription	Osteobl	bone
16	chr9:16665000-16669000	Weak transcription	NHDF-Ad	bronchial
17	chr9:16665000-16704400	Weak transcription	Aorta	Aorta
18	chr9:16666600-16667600	Enhancers	Colon Smooth Muscle	Colon
19	chr9:16667000-16670400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr9:16667200-16668000	Weak transcription	Ovary	ovary
21	chr9:16667200-16671800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:16667200-16681000	Weak transcription	Fetal Stomach	stomach
23	chr9:16667400-16668600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:16667400-16671200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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