Variant report

Variant	rs10873740
Chromosome Location	chr1:86464262-86464263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11161714	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];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11161715	0.91[CHB][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11161716	0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11161717	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];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023979	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12025292	0.91[CHB][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12025755	0.86[CHB][hapmap];0.88[ASN][1000 genomes]
rs12027751	0.82[AMR][1000 genomes]
rs12029153	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12031047	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12031072	0.84[AMR][1000 genomes]
rs12031105	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12031129	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12039529	0.91[CHB][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12040977	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12040981	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12125053	0.83[EUR][1000 genomes]
rs12127813	0.86[CHB][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12135956	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403155	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12404609	0.91[CHB][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12407101	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17405077	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17405097	0.87[MEX][hapmap]
rs17405131	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2390005	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2390006	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2390007	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2390008	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28480217	0.88[ASN][1000 genomes]
rs4272648	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4306156	0.95[CHB][hapmap];0.85[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]
rs4350224	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]
rs4912453	0.95[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.88[ASN][1000 genomes]
rs4912454	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs55892290	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55904471	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55904692	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55958413	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56278817	0.86[ASN][1000 genomes]
rs61617423	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6576795	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6656538	0.95[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs6672098	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs66724882	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6703205	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6704536	0.91[CHB][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7415711	0.84[ASN][1000 genomes]
rs7514604	0.87[ASN][1000 genomes]
rs7516083	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7547149	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551636	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10873740	COL24A1	cis	multi-tissue	Pritchard
rs10873740	SYDE2	cis	parietal	SCAN
rs10873740	COL24A1	cis	Artery Aorta	GTEx
rs10873740	COL24A1	cis	Nerve Tibial	GTEx
rs10873740	COL24A1	cis	Lymphoblastoid	GTEx
rs10873740	COL24A1	cis	Artery Tibial	GTEx
rs10873740	CLCA1	cis	cerebellum	SCAN
rs10873740	COL24A1	cis	lymphoblastoid	seeQTL

Chromatin state (count:7 , 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	chr1:86459200-86472000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:86459200-86472200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:86463600-86465000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:86464000-86464800	Enhancers	Adipose Nuclei	Adipose
7	chr1:86464000-86469800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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