Variant report

Variant	rs10462048
Chromosome Location	chr5:43258528-43258529
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:43238992..43241907-chr5:43256883..43259257,2	K562	blood:
2	chr5:43250345..43252555-chr5:43256851..43258865,2	K562	blood:

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10039048	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs10039617	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs10065852	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs10462047	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10512825	0.96[CEU][hapmap]
rs10512827	0.92[CEU][hapmap]
rs10512828	0.92[CEU][hapmap]
rs10805671	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10805672	0.96[CEU][hapmap]
rs10805673	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs10805674	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs10805675	0.92[CEU][hapmap]
rs10941620	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs10941621	0.96[CEU][hapmap]
rs10941630	0.96[CEU][hapmap]
rs10941631	0.92[CEU][hapmap]
rs11739009	0.96[CEU][hapmap]
rs11740128	0.96[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs11741246	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs11742171	0.96[CEU][hapmap]
rs11742712	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs11743622	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[TSI][hapmap]
rs11743633	0.96[CEU][hapmap]
rs11746629	0.87[EUR][1000 genomes]
rs11950040	0.92[CEU][hapmap]
rs11950448	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs11956635	0.92[CEU][hapmap]
rs11956988	0.92[CEU][hapmap]
rs12514393	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs12514399	0.96[CEU][hapmap]
rs12515072	0.96[CEU][hapmap]
rs12518032	0.96[CEU][hapmap]
rs12518127	0.92[CEU][hapmap]
rs12519554	0.96[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs13659	0.96[CEU][hapmap]
rs1545753	0.96[CEU][hapmap]
rs1548097	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs1564196	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs1564197	0.96[CEU][hapmap]
rs1564198	0.96[CEU][hapmap];0.93[CHB][hapmap];0.80[CHD][hapmap];0.82[TSI][hapmap]
rs17244818	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs2086133	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2126948	0.96[CEU][hapmap]
rs2126949	0.96[CEU][hapmap]
rs35231094	0.88[EUR][1000 genomes]
rs3733768	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.84[TSI][hapmap]
rs3733769	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs4254917	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4288122	0.96[CEU][hapmap]
rs4395639	0.96[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs4443426	0.92[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs4866734	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4866738	0.96[CEU][hapmap]
rs4866741	0.92[CEU][hapmap];0.93[CHB][hapmap]
rs4866818	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs4866820	0.92[CEU][hapmap]
rs4866822	0.96[CEU][hapmap];0.85[TSI][hapmap]
rs4866824	0.96[CEU][hapmap]
rs55647314	0.82[EUR][1000 genomes]
rs55800451	0.83[EUR][1000 genomes]
rs56023994	0.82[EUR][1000 genomes]
rs56029402	0.83[EUR][1000 genomes]
rs57392430	0.83[EUR][1000 genomes]
rs60207549	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6451684	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.84[TSI][hapmap]
rs66585077	0.88[EUR][1000 genomes]
rs67415672	0.82[EUR][1000 genomes]
rs6814	0.96[CEU][hapmap]
rs6886499	0.88[CEU][hapmap]
rs6887351	0.96[CEU][hapmap]
rs6895805	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs754527	0.93[CHB][hapmap]
rs7701391	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs7701642	0.93[CHB][hapmap]
rs7704588	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs7708779	0.96[CEU][hapmap]
rs7714027	0.92[CEU][hapmap]
rs7716091	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs7720165	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs7720681	0.92[CEU][hapmap]
rs7727047	0.89[CEU][hapmap]
rs7734293	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs9292871	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.84[TSI][hapmap]
rs9790987	0.96[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
2	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
3	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
4	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
5	nsv508352	chr5:43237830-43391062	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10462048	HMGCS1	cis	cerebellum	SCAN
rs10462048	HMGCS1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43246600-43281400	Weak transcription	Brain Hippocampus Middle	brain
2	chr5:43247600-43259800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:43247600-43261400	Weak transcription	Brain Angular Gyrus	brain
4	chr5:43257400-43274400	Weak transcription	Brain Anterior Caudate	brain

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