Variant report

Variant	rs3135299
Chromosome Location	chr6:28809050-28809051
allele	A/C/G
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:5)
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:5 , 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	chr6:28808787..28809525-chr6:28890975..28891547,2	MCF-7	breast:

No data

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

Extended variants
information (count: 111 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs13194504	1.00[AMR][1000 genomes]
rs13206458	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13217472	1.00[AMR][1000 genomes]
rs3118357	0.96[EUR][1000 genomes]
rs3118359	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3118360	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3118361	0.92[EUR][1000 genomes]
rs3118364	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3118365	0.91[EUR][1000 genomes]
rs3118366	0.94[EUR][1000 genomes]
rs3118367	0.96[EUR][1000 genomes]
rs3129791	0.84[EUR][1000 genomes]
rs3129794	0.92[EUR][1000 genomes]
rs3129797	0.92[EUR][1000 genomes]
rs3129798	0.92[EUR][1000 genomes]
rs3130837	0.96[EUR][1000 genomes]
rs3130838	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3130844	0.92[EUR][1000 genomes]
rs3130845	0.92[EUR][1000 genomes]
rs3130846	0.89[EUR][1000 genomes]
rs3130847	0.92[EUR][1000 genomes]
rs3130885	0.90[EUR][1000 genomes]
rs3130887	0.94[EUR][1000 genomes]
rs3130888	0.92[EUR][1000 genomes]
rs3130890	0.82[EUR][1000 genomes]
rs3130891	0.92[EUR][1000 genomes]
rs3130892	0.92[EUR][1000 genomes]
rs3130893	0.92[EUR][1000 genomes]
rs3130894	0.92[EUR][1000 genomes]
rs3130895	0.91[EUR][1000 genomes]
rs3130896	0.92[EUR][1000 genomes]
rs3131068	0.92[EUR][1000 genomes]
rs3131069	0.92[EUR][1000 genomes]
rs3131071	0.92[EUR][1000 genomes]
rs3131072	0.92[EUR][1000 genomes]
rs3131073	0.89[EUR][1000 genomes]
rs3131075	0.92[EUR][1000 genomes]
rs3131076	0.92[EUR][1000 genomes]
rs3131081	0.92[EUR][1000 genomes]
rs3131093	0.94[EUR][1000 genomes]
rs3131094	0.96[EUR][1000 genomes]
rs3131095	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3131096	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3131097	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3131101	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3131335	0.98[EUR][1000 genomes]
rs3131336	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3131340	0.85[EUR][1000 genomes]
rs3131341	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3131343	0.83[EUR][1000 genomes]
rs3131345	0.96[EUR][1000 genomes]
rs3132373	0.83[EUR][1000 genomes]
rs3132374	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3132376	0.96[EUR][1000 genomes]
rs3132378	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3132382	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132384	0.96[EUR][1000 genomes]
rs3132385	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132387	0.94[EUR][1000 genomes]
rs3132388	0.96[EUR][1000 genomes]
rs3132389	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132391	0.96[EUR][1000 genomes]
rs3132392	0.96[EUR][1000 genomes]
rs3132393	0.98[EUR][1000 genomes]
rs3132394	0.98[EUR][1000 genomes]
rs3132395	0.98[EUR][1000 genomes]
rs3132396	0.85[EUR][1000 genomes]
rs3135293	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135294	0.83[EUR][1000 genomes]
rs3135295	0.96[EUR][1000 genomes]
rs3135297	0.90[EUR][1000 genomes]
rs3135298	0.98[EUR][1000 genomes]
rs3135300	0.96[EUR][1000 genomes]
rs3135302	0.96[EUR][1000 genomes]
rs3135304	0.96[EUR][1000 genomes]
rs3135306	0.96[EUR][1000 genomes]
rs3135307	0.96[EUR][1000 genomes]
rs3135308	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135309	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135310	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135311	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135312	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135313	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135316	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135317	0.92[EUR][1000 genomes]
rs3135318	0.92[EUR][1000 genomes]
rs3135325	0.92[EUR][1000 genomes]
rs35044849	1.00[AMR][1000 genomes]
rs35243068	1.00[AMR][1000 genomes]
rs4324798	0.85[EUR][1000 genomes]
rs7760313	0.94[EUR][1000 genomes]
rs7761321	0.83[EUR][1000 genomes]
rs7766699	0.80[EUR][1000 genomes]
rs7767099	0.83[EUR][1000 genomes]
rs9257140	1.00[AMR][1000 genomes]
rs9257167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9257217	0.83[EUR][1000 genomes]
rs9257223	0.85[EUR][1000 genomes]
rs9257227	0.82[EUR][1000 genomes]
rs9257245	0.94[EUR][1000 genomes]
rs9257249	0.92[EUR][1000 genomes]
rs9257250	0.92[EUR][1000 genomes]
rs9257262	0.96[EUR][1000 genomes]
rs9257267	0.93[EUR][1000 genomes]
rs9257272	0.96[EUR][1000 genomes]
rs9257331	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9257345	0.87[AMR][1000 genomes];0.85[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
rs3135299	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3135299	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3135299	BTN3A2	Cis_chr	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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