Variant report

Variant	rs4400278
Chromosome Location	chr7:15474008-15474009
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10215939	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10277024	0.90[ASN][1000 genomes]
rs11972949	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11974178	0.90[ASN][1000 genomes]
rs11974364	0.86[EUR][1000 genomes]
rs11975362	0.95[ASN][1000 genomes]
rs12530705	0.98[ASN][1000 genomes]
rs12538315	0.90[ASN][1000 genomes]
rs12538341	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12699713	0.97[ASN][1000 genomes]
rs12699714	0.98[ASN][1000 genomes]
rs12699715	0.98[ASN][1000 genomes]
rs13245471	0.91[ASN][1000 genomes]
rs28498586	0.90[ASN][1000 genomes]
rs35202252	0.91[ASN][1000 genomes]
rs36101478	0.98[ASN][1000 genomes]
rs4291163	0.95[ASN][1000 genomes]
rs4321893	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4323387	0.95[ASN][1000 genomes]
rs4469360	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4472405	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4499985	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4503002	0.80[EUR][1000 genomes]
rs4598143	0.90[ASN][1000 genomes]
rs4637710	0.95[ASN][1000 genomes]
rs4640952	0.95[ASN][1000 genomes]
rs4721439	0.90[ASN][1000 genomes]
rs4721440	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6963643	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6963836	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6966311	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032569	chr7:14905287-15597069	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1021172	chr7:14944318-15548794	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv538743	chr7:14944318-15548794	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1028314	chr7:15336831-15555412	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1032866	chr7:15336831-15622515	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1033428	chr7:15343210-15554763	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1023086	chr7:15368522-15554763	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv538746	chr7:15368522-15554763	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv606295	chr7:15397449-15547950	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1031116	chr7:15428343-15568587	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1028545	chr7:15440202-15554763	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv538747	chr7:15440202-15554763	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv887728	chr7:15444355-15479473	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	n/a	n/a	inside rSNPs	diseases
14	nsv887729	chr7:15444355-15580078	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv606296	chr7:15468199-15538772	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4400278	HDAC9	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:15469800-15489200	Weak transcription	Liver	Liver
2	chr7:15474000-15474200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr7:15474000-15474200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr7:15474000-15474200	Enhancers	Adipose Nuclei	Adipose

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