Variant report

Variant	rs1418916
Chromosome Location	chr10:54730312-54730313
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	0.80[ASN][1000 genomes]
rs10740531	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10824852	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10824854	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10824856	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10824859	0.83[JPT][hapmap]
rs11003341	0.80[CEU][hapmap];0.83[JPT][hapmap]
rs11003343	0.80[CEU][hapmap];0.83[JPT][hapmap]
rs1343045	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1343046	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1343047	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1343048	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418915	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1573147	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1917190	0.80[CEU][hapmap];0.83[JPT][hapmap]
rs1917194	0.80[ASN][1000 genomes]
rs1917195	0.80[ASN][1000 genomes]
rs1917196	0.80[ASN][1000 genomes]
rs1917197	0.80[ASN][1000 genomes]
rs1917205	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1935921	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935922	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1949814	0.81[ASN][1000 genomes]
rs1984275	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066435	0.88[ASN][1000 genomes]
rs2066437	0.81[ASN][1000 genomes]
rs2066438	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2177608	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2248319	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2248678	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2253152	0.80[ASN][1000 genomes]
rs2253266	0.80[ASN][1000 genomes]
rs2264663	0.80[ASN][1000 genomes]
rs2265880	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2462479	0.80[CEU][hapmap];0.83[JPT][hapmap]
rs2488605	0.88[ASN][1000 genomes]
rs2492354	0.84[ASN][1000 genomes]
rs2891425	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2891426	0.85[ASN][1000 genomes]
rs7085307	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7092980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7097052	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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	nsv532194	chr10:53746620-54735550	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv1041940	chr10:54621342-54737528	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1418916	MSMB	cis	parietal	SCAN
rs1418916	ERCC6	cis	parietal	SCAN
rs1418916	RP11-319F12.2	cis	Thyroid	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54725000-54730400	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr10:54725600-54730400	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr10:54725800-54733200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr10:54729000-54737200	Weak transcription	Fetal Intestine Large	intestine
5	chr10:54729800-54730800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr10:54730000-54730400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr10:54730000-54731000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr10:54730000-54732200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr10:54730000-54733400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr10:54730200-54730800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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