Variant report

Variant	rs1980139
Chromosome Location	chr3:134509337-134509338
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr3:134508505-134509523	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr3:134508906-134509344	H1-neurons	neurons:	n/a	n/a
3	REST	chr3:134508536-134509479	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr3:134508801-134509435	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
EPHB1	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12488253	0.92[YRI][hapmap]
rs1447692	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1554112	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16842007	0.87[EUR][1000 genomes]
rs17695280	0.87[EUR][1000 genomes]
rs17763071	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17763226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992860	0.89[EUR][1000 genomes]
rs4955491	0.87[EUR][1000 genomes]
rs5008643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56053017	0.87[EUR][1000 genomes]
rs56173994	0.89[EUR][1000 genomes]
rs56241636	0.87[EUR][1000 genomes]
rs56242709	0.84[EUR][1000 genomes]
rs56295702	0.90[EUR][1000 genomes]
rs56358843	0.87[EUR][1000 genomes]
rs6767950	0.87[EUR][1000 genomes]
rs67899261	0.85[EUR][1000 genomes]
rs6804153	0.87[EUR][1000 genomes]
rs68091188	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs719893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs720365	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs720366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73225096	0.87[EUR][1000 genomes]
rs73227010	0.89[EUR][1000 genomes]
rs935512	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs938379	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9867555	0.94[CEU][hapmap];0.82[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877515	chr3:134460368-134591138	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1980139	EPHB1	cis	Esophagus Mucosa	GTEx
rs1980139	EPHB1	cis	Artery Tibial	GTEx
rs1980139	EPHB1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134507800-134509600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr3:134509200-134509600	Enhancers	Monocytes-CD14+_RO01746	blood

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