Variant report

Variant	rs166589
Chromosome Location	chr1:45017212-45017213
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	chr1:45012376..45014661-chr1:45014984..45017280,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10158231	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs12032772	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs12405833	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs12408210	0.84[EUR][1000 genomes]
rs12566533	0.97[ASN][1000 genomes]
rs156256	0.84[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16832091	0.83[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs172018	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs175222	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs187945	0.99[ASN][1000 genomes]
rs270699	0.92[ASN][1000 genomes]
rs270700	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270756	0.83[CEU][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs270757	0.82[EUR][1000 genomes]
rs270760	0.82[CHD][hapmap]
rs270767	0.81[EUR][1000 genomes]
rs270768	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs272565	0.87[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2924869	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2992508	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3738734	0.81[EUR][1000 genomes]
rs3850850	0.82[EUR][1000 genomes]
rs6670379	0.82[EUR][1000 genomes]
rs7525212	0.88[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv461395	chr1:44898998-45119965	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
5	nsv546144	chr1:44898998-45119965	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
7	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs166589	GUCA2A	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:44998800-45017800	Weak transcription	Right Atrium	heart
2	chr1:44998800-45022000	Weak transcription	HepG2	liver
3	chr1:45009600-45021200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:45010000-45017800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:45011000-45032800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:45012000-45023200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:45012400-45017600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:45012400-45019600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:45012400-45023400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:45012800-45018800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:45012800-45021600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:45012800-45023800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:45013200-45017400	Weak transcription	Stomach Mucosa	stomach
14	chr1:45014200-45019200	Weak transcription	Brain Anterior Caudate	brain
15	chr1:45014600-45017600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:45015400-45017600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:45015600-45017800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr1:45015600-45020800	Enhancers	Brain Substantia Nigra	brain
19	chr1:45015800-45018600	Weak transcription	Brain Angular Gyrus	brain
20	chr1:45016400-45019600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:45016600-45017600	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:45016600-45018600	Weak transcription	Brain Cingulate Gyrus	brain

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