Variant report

Variant	rs3130887
Chromosome Location	chr6:28944086-28944087
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28890727..28894097-chr6:28943047..28947323,5	MCF-7	breast:
2	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:

Variant related genes	Relation type
ENSG00000204709	Chromatin interaction
ENSG00000204713	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs13206458	0.94[EUR][1000 genomes]
rs3117146	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3118357	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	0.93[EUR][1000 genomes]
rs3118366	0.96[EUR][1000 genomes]
rs3118367	0.98[EUR][1000 genomes]
rs3129791	0.87[EUR][1000 genomes]
rs3129794	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3129797	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3129798	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3130777	0.80[EUR][1000 genomes]
rs3130837	0.89[AMR][1000 genomes];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]
rs3130888	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3130890	0.84[EUR][1000 genomes]
rs3130891	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3130892	0.94[EUR][1000 genomes]
rs3130893	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3130894	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3130895	0.93[EUR][1000 genomes]
rs3130896	0.89[AMR][1000 genomes];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	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3131085	0.91[EUR][1000 genomes]
rs3131093	0.96[EUR][1000 genomes]
rs3131094	0.98[EUR][1000 genomes]
rs3131095	0.98[EUR][1000 genomes]
rs3131096	0.98[EUR][1000 genomes]
rs3131097	0.98[EUR][1000 genomes]
rs3131101	0.91[EUR][1000 genomes]
rs3131335	0.96[EUR][1000 genomes]
rs3131336	0.98[EUR][1000 genomes]
rs3131340	0.87[EUR][1000 genomes]
rs3131341	0.87[EUR][1000 genomes]
rs3131343	0.85[EUR][1000 genomes]
rs3131345	0.98[EUR][1000 genomes]
rs3132373	0.85[EUR][1000 genomes]
rs3132374	0.94[EUR][1000 genomes]
rs3132376	0.98[EUR][1000 genomes]
rs3132378	0.91[EUR][1000 genomes]
rs3132382	0.94[EUR][1000 genomes]
rs3132384	0.98[EUR][1000 genomes]
rs3132385	0.98[EUR][1000 genomes]
rs3132387	0.96[EUR][1000 genomes]
rs3132388	0.98[EUR][1000 genomes]
rs3132389	0.98[EUR][1000 genomes]
rs3132391	0.98[EUR][1000 genomes]
rs3132392	0.98[EUR][1000 genomes]
rs3132393	0.96[EUR][1000 genomes]
rs3132394	0.96[EUR][1000 genomes]
rs3132395	0.96[EUR][1000 genomes]
rs3132396	0.87[EUR][1000 genomes]
rs3135293	0.98[EUR][1000 genomes]
rs3135294	0.85[EUR][1000 genomes]
rs3135295	0.98[EUR][1000 genomes]
rs3135297	0.92[EUR][1000 genomes]
rs3135298	0.96[EUR][1000 genomes]
rs3135299	0.94[EUR][1000 genomes]
rs3135300	0.98[EUR][1000 genomes]
rs3135302	0.98[EUR][1000 genomes]
rs3135304	0.98[EUR][1000 genomes]
rs3135306	0.98[EUR][1000 genomes]
rs3135307	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	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3135318	0.94[EUR][1000 genomes]
rs3135325	0.94[EUR][1000 genomes]
rs4324798	0.87[EUR][1000 genomes]
rs7760313	0.96[EUR][1000 genomes]
rs7761321	0.85[EUR][1000 genomes]
rs7764642	0.80[EUR][1000 genomes]
rs7766699	0.82[EUR][1000 genomes]
rs7767099	0.85[EUR][1000 genomes]
rs9257192	0.82[EUR][1000 genomes]
rs9257217	0.85[EUR][1000 genomes]
rs9257223	0.87[EUR][1000 genomes]
rs9257227	0.84[EUR][1000 genomes]
rs9257245	0.96[EUR][1000 genomes]
rs9257249	0.94[EUR][1000 genomes]
rs9257250	0.94[EUR][1000 genomes]
rs9257262	0.98[EUR][1000 genomes]
rs9257267	0.94[EUR][1000 genomes]
rs9257272	0.98[EUR][1000 genomes]
rs9257331	0.98[EUR][1000 genomes]
rs9257345	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
3	nsv1023540	chr6:28922691-29326018	Active TSS Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv538169	chr6:28922691-29326018	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv869541	chr6:28922692-29326017	Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv916439	chr6:28922697-29326087	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv462668	chr6:28922719-29342775	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv601213	chr6:28922719-29342775	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv1015796	chr6:28923980-29342825	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv462669	chr6:28936556-29337500	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
11	nsv601214	chr6:28936556-29337500	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3130887	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3130887	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3130887	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28937800-28944800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:28943000-28945000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:28943000-28945000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:28943200-28944800	Weak transcription	K562	blood
5	chr6:28943200-28945800	Weak transcription	HepG2	liver

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