Variant report

Variant	rs3118360
Chromosome Location	chr6:28792030-28792031
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28790715..28792614-chr6:28804190..28806792,2	K562	blood:
2	chr6:28783316..28785641-chr6:28791797..28793442,2	K562	blood:
3	chr6:28788096..28790497-chr6:28791295..28793656,2	K562	blood:

Variant related genes	Relation type
ENSG00000225173	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:130)

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]
rs13194504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13206458	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13217472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3118357	0.92[EUR][1000 genomes]
rs3118359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3118361	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3118364	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3118365	0.87[EUR][1000 genomes]
rs3118366	0.91[EUR][1000 genomes]
rs3118367	0.92[EUR][1000 genomes]
rs3129791	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3129794	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3130837	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3130838	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3130844	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3130845	0.89[EUR][1000 genomes]
rs3130846	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3130847	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3130885	0.87[EUR][1000 genomes]
rs3130887	0.91[EUR][1000 genomes]
rs3130888	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3130890	1.00[AFR][1000 genomes]
rs3130891	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3130892	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3130893	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3130894	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3130895	0.87[EUR][1000 genomes]
rs3130896	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3131068	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3131069	0.89[EUR][1000 genomes]
rs3131071	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3131072	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3131073	0.85[EUR][1000 genomes]
rs3131075	0.89[EUR][1000 genomes]
rs3131076	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3131081	0.89[EUR][1000 genomes]
rs3131093	0.91[EUR][1000 genomes]
rs3131094	0.92[EUR][1000 genomes]
rs3131095	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131096	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131097	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131101	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3131335	0.91[EUR][1000 genomes]
rs3131336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131340	0.96[EUR][1000 genomes]
rs3131341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3131343	0.94[EUR][1000 genomes]
rs3131345	0.92[EUR][1000 genomes]
rs3132373	0.94[EUR][1000 genomes]
rs3132374	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132376	0.92[EUR][1000 genomes]
rs3132378	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3132382	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132384	0.92[EUR][1000 genomes]
rs3132385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132387	0.91[EUR][1000 genomes]
rs3132388	0.92[EUR][1000 genomes]
rs3132389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132391	0.92[EUR][1000 genomes]
rs3132392	0.92[EUR][1000 genomes]
rs3132393	0.91[EUR][1000 genomes]
rs3132394	0.91[EUR][1000 genomes]
rs3132395	0.91[EUR][1000 genomes]
rs3132396	0.96[EUR][1000 genomes]
rs3135293	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135294	0.94[EUR][1000 genomes]
rs3135295	0.92[EUR][1000 genomes]
rs3135297	0.87[EUR][1000 genomes]
rs3135298	0.91[EUR][1000 genomes]
rs3135299	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135300	0.92[EUR][1000 genomes]
rs3135302	0.92[EUR][1000 genomes]
rs3135304	0.92[EUR][1000 genomes]
rs3135306	0.92[EUR][1000 genomes]
rs3135307	0.92[EUR][1000 genomes]
rs3135308	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135309	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135310	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135311	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135312	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135313	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135316	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135318	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3135325	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34724414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35044849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35243068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4324798	0.96[EUR][1000 genomes]
rs7760313	0.91[EUR][1000 genomes]
rs7761321	0.94[EUR][1000 genomes]
rs7764642	0.82[EUR][1000 genomes]
rs7766699	0.91[EUR][1000 genomes]
rs7767099	0.94[EUR][1000 genomes]
rs9257133	0.80[EUR][1000 genomes]
rs9257136	0.80[EUR][1000 genomes]
rs9257137	0.80[EUR][1000 genomes]
rs9257140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9257167	1.00[AMR][1000 genomes];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	0.94[EUR][1000 genomes]
rs9257223	0.96[EUR][1000 genomes]
rs9257227	0.93[EUR][1000 genomes]
rs9257245	0.91[EUR][1000 genomes]
rs9257249	0.89[EUR][1000 genomes]
rs9257250	0.89[EUR][1000 genomes]
rs9257262	0.92[EUR][1000 genomes]
rs9257267	0.89[EUR][1000 genomes]
rs9257272	0.92[EUR][1000 genomes]
rs9257331	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9257345	0.87[AMR][1000 genomes];0.81[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
rs3118360	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3118360	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3118360	BTN3A2///BTN3A3	Cis_chr	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	chr6:28791200-28794000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:28791600-28792200	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links