Variant report

Variant	rs1555629
Chromosome Location	chr13:40421628-40421629
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:40408882..40410773-chr13:40419711..40421745,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12862721	0.89[ASN][1000 genomes]
rs12865501	0.92[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12866856	0.89[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs2209234	0.99[ASN][1000 genomes]
rs2324458	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2875347	0.95[ASN][1000 genomes]
rs2985248	0.95[ASN][1000 genomes]
rs3012139	0.98[ASN][1000 genomes]
rs35781607	0.88[ASN][1000 genomes]
rs4379951	0.92[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4432144	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4447298	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4556674	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4575406	0.91[CEU][hapmap];0.92[JPT][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4941945	0.93[ASN][1000 genomes]
rs4943703	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4943705	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6563756	0.94[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6563757	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6563758	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6563764	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6563766	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6563768	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7139604	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7323371	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7325743	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7327167	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7336265	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7994425	0.90[CEU][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7997407	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs912418	0.95[ASN][1000 genomes]
rs912421	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9285137	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9548944	0.82[ASN][1000 genomes]
rs9548945	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9566480	0.93[ASN][1000 genomes]
rs9576905	0.82[EUR][1000 genomes]
rs9576907	0.99[ASN][1000 genomes]
rs9594373	0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs9603628	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9603632	0.97[ASN][1000 genomes]
rs9603634	0.94[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs968130	0.93[ASN][1000 genomes]
rs996546	0.93[ASN][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	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1040458	chr13:40249387-40638129	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1555629	CFL2	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40420400-40422000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:40421000-40421800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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