Variant report

Variant	rs12402295
Chromosome Location	chr1:171056045-171056046
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171050389..171052635-chr1:171054264..171056388,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1080197	0.85[AMR][1000 genomes]
rs10910879	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809504	0.85[AMR][1000 genomes]
rs11812061	0.84[CHB][hapmap]
rs12403297	0.85[AMR][1000 genomes]
rs12404455	0.85[AMR][1000 genomes]
rs12405599	0.85[AMR][1000 genomes]
rs17564980	0.85[AMR][1000 genomes]
rs17565336	0.92[CHB][hapmap]
rs17565983	0.85[AMR][1000 genomes]
rs17565990	0.92[AMR][1000 genomes]
rs17640463	0.84[CHB][hapmap]
rs2066529	0.85[AMR][1000 genomes]
rs2266780	0.85[AMR][1000 genomes]
rs2272797	0.84[CHB][hapmap]
rs2272800	0.84[CHB][hapmap]
rs28363530	0.81[AMR][1000 genomes]
rs28363536	0.85[AMR][1000 genomes]
rs28363537	0.85[AMR][1000 genomes]
rs28363541	0.85[AMR][1000 genomes]
rs28363571	0.85[AMR][1000 genomes]
rs28745585	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28745586	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28745588	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3754487	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs55639094	0.85[AMR][1000 genomes]
rs7054839	0.82[AMR][1000 genomes]
rs72712649	0.85[AMR][1000 genomes]
rs7886938	0.84[CHB][hapmap]
rs7887142	0.84[CHB][hapmap]
rs7889839	0.84[CHB][hapmap]

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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171053600-171056800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:171053600-171058000	Weak transcription	Small Intestine	intestine
3	chr1:171053800-171058400	Weak transcription	Fetal Intestine Large	intestine
4	chr1:171056000-171056400	Weak transcription	Liver	Liver

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