Variant report

Variant	rs10824854
Chromosome Location	chr10:54744574-54744575
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10508984	0.92[ASN][1000 genomes]
rs10740531	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10824852	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10824856	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10824859	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs11003341	0.84[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs11003343	0.84[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs1343045	0.92[EUR][1000 genomes]
rs1343046	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1343047	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1343048	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1418915	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1418916	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1539513	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1573147	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1917190	0.84[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs1917194	0.90[ASN][1000 genomes]
rs1917195	0.90[ASN][1000 genomes]
rs1917196	0.92[ASN][1000 genomes]
rs1917197	0.92[ASN][1000 genomes]
rs1917205	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1935921	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1935922	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1949814	0.89[ASN][1000 genomes]
rs1984275	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2066435	0.95[ASN][1000 genomes]
rs2066437	0.87[ASN][1000 genomes]
rs2066438	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2177608	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2248319	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2248678	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2253152	0.92[ASN][1000 genomes]
rs2253266	0.92[ASN][1000 genomes]
rs2264663	0.92[ASN][1000 genomes]
rs2265880	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2462479	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs2488605	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2492354	0.91[ASN][1000 genomes]
rs2891425	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2891426	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7085307	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7092980	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7097052	0.99[EUR][1000 genomes];0.88[ASN][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	nsv895404	chr10:54545590-54850707	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv831877	chr10:54565135-54764638	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1043809	chr10:54645158-54860817	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv540627	chr10:54645158-54860817	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv467201	chr10:54697623-54929003	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv550906	chr10:54697623-54929003	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv470939	chr10:54700783-54917339	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv508584	chr10:54704765-54747382	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv467202	chr10:54735164-54830687	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv550907	chr10:54735164-54830687	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10824854	MSMB	cis	parietal	SCAN
rs10824854	RP11-319F12.2	cis	Thyroid	GTEx
rs10824854	PCDH15	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54734600-54764600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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