Variant report

Variant	rs12091093
Chromosome Location	chr1:224785273-224785274
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224783008..224785981-chr1:224788493..224791449,2	MCF-7	breast:
2	chr1:224778814..224780539-chr1:224784357..224786736,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1036431	0.83[CEU][hapmap]
rs1039265	0.81[CEU][hapmap]
rs10915691	0.83[CEU][hapmap]
rs10915693	0.83[CEU][hapmap]
rs10915695	0.83[CEU][hapmap]
rs10916641	0.85[CHB][hapmap]
rs1106233	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12060334	0.83[CEU][hapmap]
rs12065840	0.83[CEU][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap]
rs12077707	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12079156	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12088524	0.83[CEU][hapmap]
rs12089565	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12096245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12565092	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1337538	0.91[CEU][hapmap]
rs1499289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1499291	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1499293	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1499294	0.83[CHD][hapmap];0.81[JPT][hapmap];0.84[LWK][hapmap]
rs1532557	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16850786	0.83[CEU][hapmap]
rs1985338	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4363402	0.83[CEU][hapmap]
rs58725094	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60500269	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61827075	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61827076	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6426147	0.83[CEU][hapmap]
rs6695864	0.92[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73115953	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73115958	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7415393	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7554310	0.83[CEU][hapmap]
rs883116	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs969025	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv873224	chr1:224746577-224794913	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12091093	RAB3GAP2	cis	cerebellum	SCAN
rs12091093	PYCR2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224781200-224793800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:224781600-224787200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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