Variant report

Variant	rs7411585
Chromosome Location	chr1:86457904-86457905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12025755	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12127813	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2390005	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2390006	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2390007	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2390008	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28480217	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4272648	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4306156	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4350224	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4912453	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4912454	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56278817	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6576795	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6656538	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6672098	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7415711	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7514604	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv462406	chr1:86412177-86509996	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546757	chr1:86412177-86509996	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv546758	chr1:86438327-86483632	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv3340591	chr1:86439980-86459810	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1012808	chr1:86455710-86470489	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7411585	COL24A1	cis	Artery Tibial	GTEx
rs7411585	COL24A1	cis	Artery Aorta	GTEx
rs7411585	COL24A1	cis	Nerve Tibial	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86449400-86466200	Weak transcription	Fetal Lung	lung
2	chr1:86454400-86458200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:86456200-86464600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:86457000-86458800	Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr1:86457000-86458800	Active TSS	GM12878-XiMat	blood
6	chr1:86457200-86459800	Weak transcription	Dnd41	blood
7	chr1:86457400-86458000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:86457400-86458200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:86457400-86458600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:86457600-86458800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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