Variant report

Variant	rs3118359
Chromosome Location	chr6:28793904-28793905
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28792315..28794351-chr6:28951949..28954807,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000244349	Chromatin interaction
ENSG00000227214	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:131)

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];0.96[EUR][1000 genomes]
rs13217472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3118357	1.00[EUR][1000 genomes]
rs3118360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3118361	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3118364	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3118365	0.94[EUR][1000 genomes]
rs3118366	0.98[EUR][1000 genomes]
rs3118367	1.00[EUR][1000 genomes]
rs3129791	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3129794	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130837	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3130838	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130844	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130845	0.96[EUR][1000 genomes]
rs3130846	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs3130847	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130885	0.94[EUR][1000 genomes]
rs3130887	0.98[EUR][1000 genomes]
rs3130888	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130890	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3130891	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130892	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130893	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130894	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130895	0.94[EUR][1000 genomes]
rs3130896	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131068	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131069	0.96[EUR][1000 genomes]
rs3131071	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131072	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131073	0.93[EUR][1000 genomes]
rs3131075	0.96[EUR][1000 genomes]
rs3131076	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131081	0.96[EUR][1000 genomes]
rs3131093	0.98[EUR][1000 genomes]
rs3131094	1.00[EUR][1000 genomes]
rs3131095	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131096	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131097	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131101	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131335	0.98[EUR][1000 genomes]
rs3131336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131340	0.89[EUR][1000 genomes]
rs3131341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131343	0.87[EUR][1000 genomes]
rs3131345	1.00[EUR][1000 genomes]
rs3132373	0.87[EUR][1000 genomes]
rs3132374	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132376	1.00[EUR][1000 genomes]
rs3132378	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132382	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132384	1.00[EUR][1000 genomes]
rs3132385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132387	0.98[EUR][1000 genomes]
rs3132388	1.00[EUR][1000 genomes]
rs3132389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132391	1.00[EUR][1000 genomes]
rs3132392	1.00[EUR][1000 genomes]
rs3132393	0.98[EUR][1000 genomes]
rs3132394	0.98[EUR][1000 genomes]
rs3132395	0.98[EUR][1000 genomes]
rs3132396	0.89[EUR][1000 genomes]
rs3135293	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135294	0.87[EUR][1000 genomes]
rs3135295	1.00[EUR][1000 genomes]
rs3135297	0.94[EUR][1000 genomes]
rs3135298	0.98[EUR][1000 genomes]
rs3135299	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135300	1.00[EUR][1000 genomes]
rs3135302	1.00[EUR][1000 genomes]
rs3135304	1.00[EUR][1000 genomes]
rs3135306	1.00[EUR][1000 genomes]
rs3135307	1.00[EUR][1000 genomes]
rs3135308	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135309	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135310	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135311	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135312	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135313	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135316	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135317	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3135318	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3135325	1.00[AFR][1000 genomes];0.96[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	0.89[EUR][1000 genomes]
rs7760313	0.98[EUR][1000 genomes]
rs7761321	0.87[EUR][1000 genomes]
rs7764642	0.82[EUR][1000 genomes]
rs7766699	0.84[EUR][1000 genomes]
rs7767099	0.87[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	0.87[EUR][1000 genomes]
rs9257223	0.89[EUR][1000 genomes]
rs9257227	0.85[EUR][1000 genomes]
rs9257245	0.98[EUR][1000 genomes]
rs9257249	0.96[EUR][1000 genomes]
rs9257250	0.96[EUR][1000 genomes]
rs9257262	1.00[EUR][1000 genomes]
rs9257267	0.96[EUR][1000 genomes]
rs9257272	1.00[EUR][1000 genomes]
rs9257331	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9257345	0.87[AMR][1000 genomes];0.89[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	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
3	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
4	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3118359	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3118359	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3118359	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28791200-28794000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:28792600-28794000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
3	chr6:28792600-28794000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
4	chr6:28792800-28794000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
5	chr6:28792800-28794000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
6	chr6:28793200-28794000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr6:28793600-28794000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
8	chr6:28793600-28794000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
9	chr6:28793600-28794000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:28793600-28794000	Bivalent Enhancer	HMEC	breast
11	chr6:28793800-28794000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
12	chr6:28793800-28794000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:28793800-28794000	Active TSS	K562	blood
14	chr6:28793800-28794000	Bivalent/Poised TSS	NHEK	skin

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