Variant report

Variant	rs3132394
Chromosome Location	chr6:28809038-28809039
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:28809020-28809170	MCF-7	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28806762..28809202-chr6:28828058..28830893,2	MCF-7	breast:
2	chr6:28807797..28809537-chr6:28919515..28922301,2	K562	blood:
3	chr6:28808316..28811196-chr6:28890836..28893295,2	MCF-7	breast:
4	chr6:28805049..28806796-chr6:28807543..28810088,2	MCF-7	breast:
5	chr6:28805285..28809041-chr6:28890242..28892830,8	K562	blood:
6	chr6:28808787..28809525-chr6:28890975..28891547,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000225173	TF binding region
ENSG00000225173	Chromatin interaction
ENSG00000213916	Chromatin interaction
ENSG00000204713	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1233599	0.82[EUR][1000 genomes]
rs1233600	0.82[EUR][1000 genomes]
rs1233604	0.82[EUR][1000 genomes]
rs1233618	0.82[EUR][1000 genomes]
rs1233620	0.82[EUR][1000 genomes]
rs1233623	0.82[EUR][1000 genomes]
rs13206458	0.94[EUR][1000 genomes]
rs13437309	0.90[AFR][1000 genomes]
rs3118357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3118359	0.98[EUR][1000 genomes]
rs3118360	0.91[EUR][1000 genomes]
rs3118361	0.94[EUR][1000 genomes]
rs3118364	0.93[EUR][1000 genomes]
rs3118365	0.98[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3118366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3118367	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3129791	0.86[EUR][1000 genomes]
rs3129794	0.94[EUR][1000 genomes]
rs3129797	0.94[EUR][1000 genomes]
rs3129798	0.94[EUR][1000 genomes]
rs3130837	0.98[EUR][1000 genomes]
rs3130838	0.98[EUR][1000 genomes]
rs3130844	0.94[EUR][1000 genomes]
rs3130845	0.94[EUR][1000 genomes]
rs3130846	0.91[EUR][1000 genomes]
rs3130847	0.94[EUR][1000 genomes]
rs3130885	0.92[EUR][1000 genomes]
rs3130887	0.96[EUR][1000 genomes]
rs3130888	0.94[EUR][1000 genomes]
rs3130890	0.84[EUR][1000 genomes]
rs3130891	0.94[EUR][1000 genomes]
rs3130892	0.94[EUR][1000 genomes]
rs3130893	0.94[EUR][1000 genomes]
rs3130894	0.94[EUR][1000 genomes]
rs3130895	0.92[EUR][1000 genomes]
rs3130896	0.94[EUR][1000 genomes]
rs3131068	0.94[EUR][1000 genomes]
rs3131069	0.94[EUR][1000 genomes]
rs3131071	0.94[EUR][1000 genomes]
rs3131072	0.94[EUR][1000 genomes]
rs3131073	0.91[EUR][1000 genomes]
rs3131075	0.94[EUR][1000 genomes]
rs3131076	0.94[EUR][1000 genomes]
rs3131081	0.94[EUR][1000 genomes]
rs3131093	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3131094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3131095	0.98[EUR][1000 genomes]
rs3131096	0.98[EUR][1000 genomes]
rs3131097	0.98[EUR][1000 genomes]
rs3131101	0.90[EUR][1000 genomes]
rs3131335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3131336	0.98[EUR][1000 genomes]
rs3131340	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3131341	0.87[EUR][1000 genomes]
rs3131343	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3131345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132373	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3132374	0.94[EUR][1000 genomes]
rs3132376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132378	0.90[EUR][1000 genomes]
rs3132382	0.94[EUR][1000 genomes]
rs3132384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132385	0.98[EUR][1000 genomes]
rs3132387	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132388	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132389	0.98[EUR][1000 genomes]
rs3132391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132396	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3135293	0.98[EUR][1000 genomes]
rs3135294	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3135295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3135297	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135298	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135299	0.98[EUR][1000 genomes]
rs3135300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3135302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3135304	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3135306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3135307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3135308	0.98[EUR][1000 genomes]
rs3135309	0.98[EUR][1000 genomes]
rs3135310	0.98[EUR][1000 genomes]
rs3135311	0.98[EUR][1000 genomes]
rs3135312	0.98[EUR][1000 genomes]
rs3135313	0.98[EUR][1000 genomes]
rs3135316	0.98[EUR][1000 genomes]
rs3135317	0.94[EUR][1000 genomes]
rs3135318	0.94[EUR][1000 genomes]
rs3135325	0.94[EUR][1000 genomes]
rs4324798	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6928657	0.86[AFR][1000 genomes]
rs7760313	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7761321	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7764642	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7766699	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7767099	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9257167	0.82[EUR][1000 genomes]
rs9257183	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9257184	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9257187	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9257188	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9257189	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9257192	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9257217	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9257223	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9257227	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9257245	0.98[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs9257249	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9257250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9257262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9257267	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9257272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9257331	0.98[EUR][1000 genomes]
rs9257345	0.87[EUR][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	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	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
4	esv3403240	chr6:28808022-28832799	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3132394	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3132394	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3132394	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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