Variant report

Variant	rs2390005
Chromosome Location	chr1:86458404-86458405
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10873740	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11161714	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11161715	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11161716	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11161717	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11161719	0.88[EUR][1000 genomes]
rs12023979	0.89[ASN][1000 genomes]
rs12025292	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12025755	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12029153	0.89[ASN][1000 genomes]
rs12031047	0.89[ASN][1000 genomes]
rs12031105	0.89[ASN][1000 genomes]
rs12031129	0.89[ASN][1000 genomes]
rs12039529	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12040977	0.88[ASN][1000 genomes]
rs12040981	0.88[ASN][1000 genomes]
rs12127813	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135956	0.88[ASN][1000 genomes]
rs12403155	0.89[ASN][1000 genomes]
rs12404609	0.89[ASN][1000 genomes]
rs12407101	0.88[ASN][1000 genomes]
rs1324899	0.89[EUR][1000 genomes]
rs17405131	0.86[ASN][1000 genomes]
rs2390006	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2390007	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2390008	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28480217	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4272648	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4306156	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4350224	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912453	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912454	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55892290	0.88[ASN][1000 genomes]
rs55904471	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs55904692	0.80[ASN][1000 genomes]
rs55958413	0.88[ASN][1000 genomes]
rs56278817	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61617423	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6576795	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656538	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6672098	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66724882	0.89[ASN][1000 genomes]
rs6704536	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7411585	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7415711	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7514604	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7516083	0.89[ASN][1000 genomes]
rs7547149	0.88[ASN][1000 genomes]
rs7551636	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2390005	COL24A1	cis	Thyroid	GTEx
rs2390005	COL24A1	cis	Artery Tibial	GTEx
rs2390005	COL24A1	cis	Nerve Tibial	GTEx
rs2390005	COL24A1	cis	Artery Aorta	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86449400-86466200	Weak transcription	Fetal Lung	lung
2	chr1:86456200-86464600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:86457000-86458800	Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr1:86457000-86458800	Active TSS	GM12878-XiMat	blood
5	chr1:86457200-86459800	Weak transcription	Dnd41	blood
6	chr1:86457400-86458600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:86457600-86458800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:86458000-86459000	Active TSS	Primary hematopoietic stem cells	blood
9	chr1:86458000-86459200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:86458200-86458800	Active TSS	Muscle Satellite Cultured Cells	--
11	chr1:86458400-86458800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:86458400-86458800	Active TSS	Osteobl	bone
13	chr1:86458400-86459000	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr1:86458400-86459000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:86458400-86459000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:86458400-86459000	Active TSS	Adipose Nuclei	Adipose
17	chr1:86458400-86459200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:86458400-86459200	Active TSS	Right Atrium	heart

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