Variant report

Variant	rs12040977
Chromosome Location	chr1:86466085-86466086
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10873740	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]
rs10873744	0.84[CEU][hapmap]
rs11161713	0.82[EUR][1000 genomes]
rs11161714	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11161715	0.87[CHB][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11161716	0.87[CHB][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11161717	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12023979	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12025292	0.87[CHB][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12025755	0.82[CHB][hapmap];0.88[ASN][1000 genomes]
rs12027751	0.80[AMR][1000 genomes]
rs12029153	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12031047	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12031072	0.80[AMR][1000 genomes]
rs12031105	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12031129	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12039529	0.87[CHB][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12040981	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118004	0.82[EUR][1000 genomes]
rs12127813	0.82[CHB][hapmap];0.88[ASN][1000 genomes]
rs12134342	0.82[EUR][1000 genomes]
rs12135956	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12403155	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12404609	0.87[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12407101	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17405077	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17405097	0.81[EUR][1000 genomes]
rs17405131	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2390005	0.88[ASN][1000 genomes]
rs2390006	0.86[ASN][1000 genomes]
rs2390007	0.88[ASN][1000 genomes]
rs2390008	0.87[ASN][1000 genomes]
rs28480217	0.88[ASN][1000 genomes]
rs4272648	0.88[ASN][1000 genomes]
rs4306156	0.91[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs4350224	0.91[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs489385	0.82[EUR][1000 genomes]
rs4912453	0.91[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs4912454	0.88[ASN][1000 genomes]
rs516213	0.84[CEU][hapmap]
rs535637	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs55892290	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55904471	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55904692	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55958413	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56278817	0.88[ASN][1000 genomes]
rs569419	0.85[CEU][hapmap]
rs582141	0.82[CEU][hapmap]
rs583315	0.84[CEU][hapmap]
rs613060	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs61617423	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs640303	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs648833	0.82[EUR][1000 genomes]
rs6576795	0.88[ASN][1000 genomes]
rs662369	0.82[EUR][1000 genomes]
rs6656538	0.91[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.86[ASN][1000 genomes]
rs6672098	0.88[ASN][1000 genomes]
rs66724882	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6703205	0.87[ASN][1000 genomes]
rs6704536	0.87[CHB][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7415711	0.83[ASN][1000 genomes]
rs7514604	0.86[ASN][1000 genomes]
rs7516083	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7537787	0.82[EUR][1000 genomes]
rs7547149	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7551636	0.81[ASN][1000 genomes]
rs997110	0.81[CEU][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12040977	COL24A1	cis	Artery Aorta	GTEx
rs12040977	COL24A1	cis	Artery Tibial	GTEx
rs12040977	COL24A1	cis	Nerve Tibial	GTEx
rs12040977	COL24A1	cis	multi-tissue	Pritchard
rs12040977	COL24A1	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86449400-86466200	Weak transcription	Fetal Lung	lung
2	chr1:86459200-86472000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:86459200-86472200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:86464000-86469800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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