Variant report

Variant	rs7660788
Chromosome Location	chr4:78754162-78754163
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:78752734..78755481-chr4:78760331..78761862,2	MCF-7	breast:
2	chr4:78754144..78756097-chr4:78756156..78760285,3	MCF-7	breast:
3	chr4:78753319..78755549-chr4:78763933..78765512,2	MCF-7	breast:
4	chr4:78751560..78754519-chr4:78789849..78792401,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10005531	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10005935	0.85[CHB][hapmap];1.00[YRI][hapmap]
rs10018117	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10019920	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs10026176	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10027634	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10027739	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs10030568	0.92[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap]
rs10049674	0.92[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs10222901	0.83[YRI][hapmap]
rs1106457	0.85[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11931686	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11942975	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12509847	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12510593	0.80[YRI][hapmap]
rs13131331	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1587563	0.90[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17002804	0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1809919	0.80[AFR][1000 genomes]
rs2036455	0.84[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs2036457	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs2102116	0.83[YRI][hapmap]
rs28436599	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2866688	0.83[YRI][hapmap]
rs2866690	0.82[YRI][hapmap]
rs28685099	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4128860	0.92[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4304001	0.83[YRI][hapmap]
rs4328941	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4388114	0.83[YRI][hapmap]
rs4410552	0.89[YRI][hapmap]
rs4859512	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs4859513	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs4859882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859890	0.93[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6533225	0.81[CEU][hapmap];0.90[CHB][hapmap]
rs6533355	0.81[EUR][1000 genomes]
rs6533372	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs67814821	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6811439	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6814088	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6816134	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6820725	0.80[EUR][1000 genomes]
rs6825492	0.85[ASN][1000 genomes]
rs6835993	0.86[CHB][hapmap]
rs6849145	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6850111	0.82[YRI][hapmap]
rs7436080	0.92[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap]
rs7682450	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7687812	0.83[YRI][hapmap]
rs873280	0.85[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs924684	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs924685	0.93[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9654194	0.95[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9994366	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829976	chr4:78576657-78757798	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	esv1818157	chr4:78678104-78849088	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	esv1824966	chr4:78747771-78823070	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv516836	chr4:78748977-78981919	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv594704	chr4:78748977-78981919	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7660788	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78753400-78754600	Enhancers	NHEK	skin
2	chr4:78753600-78755000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:78753600-78755000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:78753600-78755000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:78753600-78755200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr4:78754000-78755000	Enhancers	HMEC	breast

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