Variant report

Variant	rs10054076
Chromosome Location	chr5:96701779-96701780
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10035513	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10035565	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10051764	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10054816	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10055299	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10061167	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10063468	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10069958	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10075933	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10076852	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12332533	0.88[EUR][1000 genomes]
rs13354008	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13354043	0.97[EUR][1000 genomes]
rs13354523	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13356343	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13360631	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13361168	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][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]
rs17082247	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17087492	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17087493	1.00[EUR][1000 genomes]
rs17087516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28385871	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28639483	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28750798	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28800648	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28837479	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60166438	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62377147	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62377152	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62377153	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62377268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377297	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377298	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377304	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377305	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377306	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377307	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377308	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377309	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377311	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377347	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377348	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377349	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377350	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377351	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377352	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377353	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377354	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377355	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377356	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377357	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62377359	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62378309	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62378342	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62378343	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62378462	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62378463	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62378484	0.83[EUR][1000 genomes]
rs6875798	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6877080	0.83[EUR][1000 genomes]
rs6879548	0.88[EUR][1000 genomes]
rs6882550	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6884708	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6886219	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6888385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7714487	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7721324	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7722625	0.81[EUR][1000 genomes]
rs7736813	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1019790	chr5:96471680-96980633	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv537812	chr5:96471680-96980633	ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv534326	chr5:96531217-97283481	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv882394	chr5:96538585-97108559	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1032548	chr5:96565121-97046804	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv537813	chr5:96565121-97046804	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv830415	chr5:96597763-96764157	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv598964	chr5:96612401-96705762	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1025654	chr5:96613448-96817528	ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10054076	CAPS	trans	brain	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96699400-96702000	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr5:96699600-96703200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:96700600-96702000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr5:96700600-96702200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr5:96701000-96701800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr5:96701000-96702000	Enhancers	H1 Cell Line	embryonic stem cell
7	chr5:96701000-96702000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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