Variant report

Variant	rs4350224
Chromosome Location	chr1:86458297-86458298
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10873740	0.95[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11161714	0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11161715	0.87[CHB][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11161716	0.86[CHB][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11161717	0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11161719	0.89[EUR][1000 genomes]
rs12023979	0.89[ASN][1000 genomes]
rs12025292	0.86[CHB][hapmap];0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12025755	0.91[CHB][hapmap];0.93[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	0.86[CHB][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12040977	0.91[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs12040981	0.91[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs12127813	0.91[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135956	0.88[ASN][1000 genomes]
rs12403155	0.89[ASN][1000 genomes]
rs12404609	0.87[CHB][hapmap];0.89[ASN][1000 genomes]
rs12407101	0.88[ASN][1000 genomes]
rs1324899	0.89[EUR][1000 genomes]
rs17405077	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs17405131	0.86[ASN][1000 genomes]
rs2390005	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2390006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2390007	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2390008	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28480217	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4272648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4306156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912453	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55892290	0.88[ASN][1000 genomes]
rs55904471	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs55904692	0.80[ASN][1000 genomes]
rs55958413	0.88[ASN][1000 genomes]
rs56278817	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61617423	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6576795	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6672098	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66724882	0.89[ASN][1000 genomes]
rs6704536	0.87[CHB][hapmap];0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7411585	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7415711	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7514604	0.95[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	0.91[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs7551636	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4350224	COL24A1	cis	Artery Aorta	GTEx
rs4350224	COL24A1	cis	Artery Tibial	GTEx
rs4350224	COL24A1	cis	Thyroid	GTEx
rs4350224	CCBL2	cis	cerebellum	SCAN
rs4350224	COL24A1	cis	lymphoblastoid	seeQTL
rs4350224	COL24A1	cis	Nerve Tibial	GTEx

Chromatin state (count:13 , 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	chr1:86458200-86458400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:86458200-86458400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:86458200-86458400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:86458200-86458800	Active TSS	Muscle Satellite Cultured Cells	--

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