Variant report

Variant	rs13098635
Chromosome Location	chr3:139748739-139748740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1025175	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13067861	0.81[TSI][hapmap]
rs13315308	1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs13322299	1.00[JPT][hapmap]
rs1365152	0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes]
rs17398553	0.92[AMR][1000 genomes]
rs17398740	1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2114167	0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs2162212	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2350274	0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.84[AMR][1000 genomes]
rs35229182	0.94[ASN][1000 genomes]
rs6439892	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs67276954	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71314533	0.92[AMR][1000 genomes]
rs7433787	1.00[ASN][1000 genomes]
rs7433809	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615793	0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs9289595	1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes]
rs9813297	1.00[ASW][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9818578	1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9820731	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9824570	0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes]
rs9827738	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9833263	1.00[JPT][hapmap];0.89[TSI][hapmap];0.93[ASN][1000 genomes]
rs9845143	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9851415	0.92[AMR][1000 genomes]
rs9863333	1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874196	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9878201	1.00[JPT][hapmap];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	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv998423	chr3:139526446-139947336	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv829738	chr3:139670836-139851945	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv877545	chr3:139738645-139821310	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13098635	ESYT3	cis	cerebellum	SCAN
rs13098635	SLC25A36	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139739600-139754400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:139744800-139750000	Weak transcription	Ovary	ovary
3	chr3:139747600-139749600	Weak transcription	HSMMtube	muscle

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