Variant report

Variant	rs12086252
Chromosome Location	chr1:221772054-221772055
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	chr1:221766078..221767726-chr1:221770721..221773346,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10082031	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10082119	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10449312	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10495171	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11118769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11118771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12058091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12060691	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12063275	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12063464	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12064012	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12064162	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12067974	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12075242	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12079769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12081273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12081326	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12082182	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12082815	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12082874	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12084065	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12086291	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12088112	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12089796	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12092891	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12093053	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12094911	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12095828	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12095905	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13376358	0.88[EUR][1000 genomes]
rs17010395	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17010397	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17010409	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17010428	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17010434	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17010457	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17010463	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1890243	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1973728	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28515661	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56971545	1.00[EUR][1000 genomes]
rs57255089	1.00[EUR][1000 genomes]
rs58173559	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58482927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59383649	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59680640	1.00[EUR][1000 genomes]
rs59837278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60152531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60217573	1.00[EUR][1000 genomes]
rs61079406	1.00[EUR][1000 genomes]
rs61221236	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73117552	0.88[EUR][1000 genomes]
rs74145360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74145363	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74145364	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74145365	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74145366	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74145367	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74145373	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74145375	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74145376	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74145378	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74145394	0.93[AFR][1000 genomes]
rs74145400	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9308402	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv873200	chr1:221644180-221843191	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1009838	chr1:221692621-221773945	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv535301	chr1:221692621-221773945	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv1808490	chr1:221743979-221779026	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv1814250	chr1:221746140-221772404	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1011037	chr1:221756526-221809552	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221771200-221773000	Enhancers	Brain Cingulate Gyrus	brain
2	chr1:221771200-221773400	Enhancers	Brain Substantia Nigra	brain
3	chr1:221771800-221772200	Flanking Active TSS	Brain Hippocampus Middle	brain
4	chr1:221771800-221772200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
5	chr1:221771800-221772600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:221771800-221784600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:221772000-221773000	Weak transcription	Brain Angular Gyrus	brain
8	chr1:221772000-221779000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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