Variant report

Variant	rs259833
Chromosome Location	chr2:180706328-180706329
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:180697026..180699896-chr2:180705650..180708149,2	MCF-7	breast:
2	chr2:180706168..180708341-chr2:180711093..180713264,3	K562	blood:
3	chr2:180704558..180706677-chr2:180713016..180714537,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10153833	0.96[CEU][hapmap]
rs10930887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12053220	0.90[JPT][hapmap]
rs12053223	0.90[JPT][hapmap]
rs12053553	0.90[JPT][hapmap]
rs12328338	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs12465175	1.00[JPT][hapmap]
rs13014995	0.96[CEU][hapmap]
rs1352111	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs1383413	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]
rs1383414	0.81[EUR][1000 genomes]
rs1486233	0.97[ASN][1000 genomes]
rs165373	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs165374	0.96[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs165379	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs165380	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs165381	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16867045	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs187745	0.96[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs194674	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2170240	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2219670	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs2367797	0.89[CEU][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs259831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259849	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2630539	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28520865	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs357711	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs357712	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs357714	0.96[CEU][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap]
rs56152328	0.90[ASN][1000 genomes]
rs6433810	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6433811	0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs6725456	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs6752731	0.89[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7557122	0.89[CEU][hapmap];0.95[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7588035	0.89[CEU][hapmap]
rs7597666	0.89[CEU][hapmap];0.95[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.95[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
rs259833	EVX2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180703200-180706400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:180703400-180707400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:180705800-180706600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr2:180706200-180706800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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