Variant report

Variant	rs9257227
Chromosome Location	chr6:28787384-28787385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1233579	0.80[EUR][1000 genomes]
rs1233580	0.80[EUR][1000 genomes]
rs1233581	0.80[EUR][1000 genomes]
rs1233583	0.80[EUR][1000 genomes]
rs1233593	0.80[EUR][1000 genomes]
rs1233594	0.80[EUR][1000 genomes]
rs1233599	0.84[EUR][1000 genomes]
rs1233600	0.84[EUR][1000 genomes]
rs1233604	0.84[EUR][1000 genomes]
rs1233618	0.84[EUR][1000 genomes]
rs1233620	0.84[EUR][1000 genomes]
rs1233623	0.84[EUR][1000 genomes]
rs1238262	0.80[EUR][1000 genomes]
rs1311912	0.80[EUR][1000 genomes]
rs1311913	0.80[EUR][1000 genomes]
rs13206458	0.82[EUR][1000 genomes]
rs3118357	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3118359	0.85[EUR][1000 genomes]
rs3118360	0.93[EUR][1000 genomes]
rs3118361	0.82[EUR][1000 genomes]
rs3118364	0.81[EUR][1000 genomes]
rs3118365	0.80[EUR][1000 genomes]
rs3118366	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3118367	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3129794	0.82[EUR][1000 genomes]
rs3130837	0.85[EUR][1000 genomes]
rs3130838	0.85[EUR][1000 genomes]
rs3130844	0.82[EUR][1000 genomes]
rs3130845	0.82[EUR][1000 genomes]
rs3130847	0.82[EUR][1000 genomes]
rs3130885	0.80[EUR][1000 genomes]
rs3130887	0.84[EUR][1000 genomes]
rs3130888	0.82[EUR][1000 genomes]
rs3130891	0.82[EUR][1000 genomes]
rs3130892	0.82[EUR][1000 genomes]
rs3130893	0.82[EUR][1000 genomes]
rs3130894	0.82[EUR][1000 genomes]
rs3130895	0.80[EUR][1000 genomes]
rs3130896	0.82[EUR][1000 genomes]
rs3131068	0.82[EUR][1000 genomes]
rs3131069	0.82[EUR][1000 genomes]
rs3131071	0.82[EUR][1000 genomes]
rs3131072	0.82[EUR][1000 genomes]
rs3131075	0.82[EUR][1000 genomes]
rs3131076	0.82[EUR][1000 genomes]
rs3131081	0.82[EUR][1000 genomes]
rs3131093	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3131094	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3131095	0.85[EUR][1000 genomes]
rs3131096	0.85[EUR][1000 genomes]
rs3131097	0.85[EUR][1000 genomes]
rs3131335	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3131336	0.85[EUR][1000 genomes]
rs3131340	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3131341	0.96[EUR][1000 genomes]
rs3131343	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3131345	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3132373	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3132374	0.82[EUR][1000 genomes]
rs3132376	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3132382	0.82[EUR][1000 genomes]
rs3132384	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3132385	0.85[EUR][1000 genomes]
rs3132387	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3132388	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3132389	0.85[EUR][1000 genomes]
rs3132391	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3132392	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3132393	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3132394	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3132395	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3132396	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135293	0.85[EUR][1000 genomes]
rs3135294	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3135295	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3135297	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3135298	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3135299	0.82[EUR][1000 genomes]
rs3135300	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3135302	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3135304	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3135306	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3135307	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3135308	0.85[EUR][1000 genomes]
rs3135309	0.85[EUR][1000 genomes]
rs3135310	0.85[EUR][1000 genomes]
rs3135311	0.85[EUR][1000 genomes]
rs3135312	0.85[EUR][1000 genomes]
rs3135313	0.85[EUR][1000 genomes]
rs3135316	0.85[EUR][1000 genomes]
rs3135318	0.82[EUR][1000 genomes]
rs3135325	0.82[EUR][1000 genomes]
rs4324798	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6928657	0.81[AFR][1000 genomes]
rs7760313	0.84[EUR][1000 genomes]
rs7761321	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7764642	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7766699	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7767099	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9257133	0.80[EUR][1000 genomes]
rs9257136	0.80[EUR][1000 genomes]
rs9257137	0.80[EUR][1000 genomes]
rs9257140	0.80[EUR][1000 genomes]
rs9257167	0.84[EUR][1000 genomes]
rs9257183	0.84[EUR][1000 genomes]
rs9257184	0.84[EUR][1000 genomes]
rs9257187	0.84[EUR][1000 genomes]
rs9257188	0.84[EUR][1000 genomes]
rs9257189	0.84[EUR][1000 genomes]
rs9257192	0.84[EUR][1000 genomes]
rs9257217	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9257223	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9257245	0.84[EUR][1000 genomes]
rs9257249	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9257250	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9257262	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9257267	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9257272	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9257331	0.85[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	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv883517	chr6:28751727-28802149	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9257227	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs9257227	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9257227	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28786000-28792200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:28786400-28791000	Weak transcription	A549	lung
3	chr6:28786400-28791200	Weak transcription	K562	blood

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