Variant report

Variant	rs1383413
Chromosome Location	chr2:180717633-180717634
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:180709707..180712515-chr2:180716241..180718781,2	K562	blood:
2	chr2:180711911..180714659-chr2:180717451..180719062,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10153833	0.83[CEU][hapmap]
rs10930887	0.88[CEU][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12053220	1.00[JPT][hapmap]
rs12053223	1.00[JPT][hapmap]
rs12053553	1.00[JPT][hapmap]
rs12328338	0.81[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.86[ASN][1000 genomes]
rs12465175	0.90[JPT][hapmap]
rs13014995	0.84[CEU][hapmap];0.81[AMR][1000 genomes]
rs1352111	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs1383414	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1486233	0.86[ASN][1000 genomes]
rs165373	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs165374	0.84[CEU][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs165379	0.84[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs165380	0.84[CEU][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs165381	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16867045	0.93[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs187745	0.92[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs194674	0.88[CEU][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2170240	0.94[ASN][1000 genomes]
rs2219670	0.81[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.86[ASN][1000 genomes]
rs2367797	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs259831	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs259833	0.88[CEU][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs259849	0.91[ASN][1000 genomes]
rs2630539	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28520865	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs357711	0.90[EUR][1000 genomes]
rs357712	0.84[CEU][hapmap];0.92[EUR][1000 genomes]
rs357714	0.84[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs56152328	0.81[ASN][1000 genomes]
rs6433810	0.90[JPT][hapmap]
rs6433811	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6725456	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6752731	0.84[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7557122	0.84[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs7597666	0.84[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002305	chr2:180568558-180812846	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428731	chr2:180629389-180805171	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv875472	chr2:180696414-181024926	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
4	nsv875473	chr2:180696414-181055597	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1383413	EVX2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180706800-180724800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:180717400-180718200	Enhancers	Liver	Liver

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