Variant report

Variant	rs9876980
Chromosome Location	chr3:160354862-160354863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10513556	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1141023	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17236452	0.84[ASN][1000 genomes]
rs1882124	1.00[ASN][1000 genomes]
rs1882128	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1920645	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1920648	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920654	1.00[ASN][1000 genomes]
rs2029361	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2272489	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs35281166	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs41272955	0.84[ASN][1000 genomes]
rs41272957	0.84[ASN][1000 genomes]
rs4254702	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4434183	0.87[ASN][1000 genomes]
rs4635753	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4679883	0.84[ASN][1000 genomes]
rs4679887	0.87[ASN][1000 genomes]
rs4679894	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4680582	0.84[ASN][1000 genomes]
rs4680590	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs55853078	0.84[ASN][1000 genomes]
rs56051094	0.84[ASN][1000 genomes]
rs56322040	0.84[ASN][1000 genomes]
rs6780828	1.00[ASN][1000 genomes]
rs6806971	0.87[ASN][1000 genomes]
rs73154591	0.84[ASN][1000 genomes]
rs73154596	0.84[ASN][1000 genomes]
rs73154600	0.84[ASN][1000 genomes]
rs73154602	0.84[ASN][1000 genomes]
rs73155903	0.84[ASN][1000 genomes]
rs73155920	0.87[ASN][1000 genomes]
rs73155922	0.87[ASN][1000 genomes]
rs73155924	0.87[ASN][1000 genomes]
rs7622031	0.84[ASN][1000 genomes]
rs9812531	0.89[EUR][1000 genomes]
rs9826290	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9845172	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847144	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	nsv877703	chr3:160325458-160398885	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	esv2757019	chr3:160351021-160380161	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv2759194	chr3:160351021-160380161	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv2755769	chr3:160352298-160359298	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9876980	LXN	cis	parietal	SCAN
rs9876980	IFT80	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160354600-160355200	Enhancers	HUVEC	blood vessel
2	chr3:160354800-160355000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:160354800-160355400	Enhancers	NH-A	brain
4	chr3:160354800-160355800	Enhancers	Hela-S3	cervix

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