Variant report

Variant	rs1561569
Chromosome Location	chr2:188942126-188942127
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12466815	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13002178	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13035162	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1371523	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1371524	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1371525	1.00[ASN][1000 genomes]
rs1439877	1.00[ASN][1000 genomes]
rs1439878	1.00[ASN][1000 genomes]
rs1439879	1.00[ASN][1000 genomes]
rs1439912	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1595765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17264870	0.93[ASN][1000 genomes]
rs1821997	1.00[ASN][1000 genomes]
rs1837456	1.00[ASN][1000 genomes]
rs2350560	1.00[ASN][1000 genomes]
rs2350561	0.93[ASN][1000 genomes]
rs34938766	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62180771	1.00[ASN][1000 genomes]
rs62180775	1.00[ASN][1000 genomes]
rs62180807	1.00[ASN][1000 genomes]
rs62180809	0.93[ASN][1000 genomes]
rs62180813	0.93[ASN][1000 genomes]
rs6724481	0.93[ASN][1000 genomes]
rs7563498	1.00[ASN][1000 genomes]
rs7596880	1.00[ASN][1000 genomes]
rs893747	1.00[ASN][1000 genomes]
rs977699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533353	chr2:188498301-189024655	Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv875602	chr2:188923773-189016215	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv875603	chr2:188923773-189025977	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv584044	chr2:188928433-189016215	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1002714	chr2:188934297-189025084	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1561569	ORMDL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:188938800-188942400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:188939800-188942400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr2:188939800-188944000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:188941400-188943000	Enhancers	GM12878-XiMat	blood

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