Variant report

Variant	rs2488405
Chromosome Location	chr1:197760172-197760173
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	chr1:197743382..197746114-chr1:197759045..197761455,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213047	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10922288	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10922292	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10922293	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11801596	0.82[AFR][1000 genomes]
rs11803693	0.81[AFR][1000 genomes]
rs11803984	0.82[AFR][1000 genomes]
rs11804036	0.82[AFR][1000 genomes]
rs11805085	0.81[AFR][1000 genomes]
rs11806071	0.82[AFR][1000 genomes]
rs11808449	0.82[AFR][1000 genomes]
rs12117095	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12125742	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12127369	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12129043	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12137370	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12562684	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12740849	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12740869	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1342694	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1342696	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1499592	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1499593	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1539413	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1578718	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1578719	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1592220	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1592221	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1622740	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1622904	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1623752	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16841983	0.82[AFR][1000 genomes]
rs1747812	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1747813	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1747814	0.81[AMR][1000 genomes]
rs1747815	0.83[AMR][1000 genomes]
rs1747818	0.81[ASN][1000 genomes]
rs1747820	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1747821	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1747822	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1747823	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1747824	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1747825	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1747828	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1775443	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1775444	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1775445	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1775446	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1775447	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1775454	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1775456	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1775458	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1775459	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1775460	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1775461	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1775462	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1775463	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1775464	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1775465	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1775466	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1775467	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1775468	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1775469	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1924518	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2133535	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2133536	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2265664	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2266033	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2266034	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2266035	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2454640	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2454641	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2454642	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2477060	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2477063	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2477065	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2477066	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2477069	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2488394	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2488395	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2488396	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2488402	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2488403	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2488404	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2497862	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2497863	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2649556	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2649557	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2797147	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34548547	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35170775	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35191270	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35432263	0.82[AFR][1000 genomes]
rs4915248	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4915566	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55873039	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61830571	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61830598	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6658157	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6697696	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6704186	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7526770	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7538522	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427908	chr1:197611569-197767362	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv947369	chr1:197750549-197778118	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197757200-197768000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:197757200-197769600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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