Variant report

Variant	rs649935
Chromosome Location	chr6:76303749-76303750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:76301594..76304347-chr6:76310698..76312348,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112701	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1018103	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10943253	0.88[CEU][hapmap]
rs10943273	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10943274	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12196018	0.86[CHB][hapmap]
rs12199457	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12524436	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12525161	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13191639	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13214795	0.91[CEU][hapmap]
rs1414597	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs2133192	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2647399	0.92[CEU][hapmap]
rs2647401	0.92[CEU][hapmap]
rs2647402	0.92[CEU][hapmap]
rs2647409	0.81[EUR][1000 genomes]
rs2647412	0.92[CEU][hapmap]
rs2647415	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2647416	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2647418	0.92[CEU][hapmap]
rs2748953	0.92[CEU][hapmap]
rs2783351	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2784730	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2784732	0.81[EUR][1000 genomes]
rs2784733	0.81[EUR][1000 genomes]
rs2842535	0.91[CEU][hapmap]
rs2842539	0.81[EUR][1000 genomes]
rs2842563	0.87[CEU][hapmap]
rs34239015	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs478934	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs486777	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs570939	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs575720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6453832	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6907247	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6911868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6936251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6936565	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7356806	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7747801	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7747947	0.82[CHB][hapmap]
rs775071	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9294001	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9350598	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9352237	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9352238	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9359137	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9443180	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9447510	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs9447513	0.80[EUR][1000 genomes]
rs9447514	0.81[EUR][1000 genomes]
rs9447522	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9447523	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9447524	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9885866	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv1022428	chr6:76023118-76575620	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
4	nsv538312	chr6:76023118-76575620	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
5	nsv1032245	chr6:76045537-76545703	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats 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 miRNA	47 gene(s)	inside rSNPs	diseases
6	nsv538313	chr6:76045537-76545703	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
7	nsv1019328	chr6:76154751-76604197	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
8	nsv538314	chr6:76154751-76604197	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
9	nsv1023331	chr6:76238459-76482117	Strong transcription ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv538315	chr6:76238459-76482117	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv1017542	chr6:76238459-76537447	Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
12	nsv1031745	chr6:76257913-76493355	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
13	nsv538316	chr6:76257913-76493355	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
14	nsv533100	chr6:76257914-76493354	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
15	nsv1023749	chr6:76287578-76482117	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
16	nsv538317	chr6:76287578-76482117	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs649935	SENP6	cis	Whole Blood	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76298800-76305600	Weak transcription	Fetal Intestine Small	intestine
2	chr6:76303200-76305600	Weak transcription	Fetal Intestine Large	intestine

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