Variant report

Variant	rs9885866
Chromosome Location	chr6:76308489-76308490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr6:76308402-76308508	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:76306113..76308673-chr6:76313720..76315996,2	K562	blood:
2	chr6:76307687..76309384-chr6:76493357..76494955,2	K562	blood:
3	chr6:76295830..76298564-chr6:76308288..76310113,2	MCF-7	breast:

Variant related genes	Relation type
SENP6	TF binding region
ENSG00000220730	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10806043	0.81[ASN][1000 genomes]
rs10943253	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs10943273	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10943274	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12199441	0.91[ASN][1000 genomes]
rs12199457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12213227	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12524436	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12525161	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13191639	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13214795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1336043	0.86[JPT][hapmap]
rs1414597	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2647399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2647400	0.81[JPT][hapmap]
rs2647401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2647402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2647403	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2647409	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2647412	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2647413	0.88[EUR][1000 genomes]
rs2647415	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2647418	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2647419	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2703662	0.86[JPT][hapmap]
rs2748953	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2748965	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2756039	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2783351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2784730	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2784732	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2784733	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2808182	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2808186	0.87[JPT][hapmap]
rs2808187	0.87[JPT][hapmap]
rs2842535	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2842539	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2842563	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2842571	0.87[EUR][1000 genomes]
rs2842572	0.85[EUR][1000 genomes]
rs2951917	0.82[JPT][hapmap]
rs2951920	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2998367	0.81[JPT][hapmap]
rs34239015	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4708189	0.85[YRI][hapmap]
rs478934	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs570939	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs575720	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6453832	0.85[AMR][1000 genomes]
rs649935	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6911868	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs6936251	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs7356806	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9294001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9343290	0.87[JPT][hapmap]
rs9352237	0.92[CEU][hapmap]
rs9443180	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9447510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9447513	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9447514	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9447522	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9447523	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9447524	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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
17	nsv1021090	chr6:76306100-76759397	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
18	nsv538318	chr6:76306100-76759397	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9885866	SENP6	cis	Whole Blood	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76306000-76310000	Weak transcription	Fetal Intestine Large	intestine
2	chr6:76306200-76309000	Weak transcription	Fetal Intestine Small	intestine
3	chr6:76306800-76310400	Weak transcription	HepG2	liver
4	chr6:76307200-76308600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:76307600-76308600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:76307800-76309000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:76307800-76309200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr6:76308000-76308600	Enhancers	Duodenum Mucosa	Duodenum
9	chr6:76308000-76308800	Active TSS	Aorta	Aorta
10	chr6:76308000-76308800	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr6:76308000-76309200	Active TSS	Stomach Smooth Muscle	stomach
12	chr6:76308200-76308600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr6:76308200-76308600	Enhancers	Brain Angular Gyrus	brain
14	chr6:76308200-76308800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr6:76308200-76308800	Active TSS	Ovary	ovary
16	chr6:76308200-76309000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr6:76308200-76309000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:76308200-76309000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr6:76308200-76309000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:76308200-76309000	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr6:76308400-76308600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:76308400-76308800	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr6:76308400-76308800	Active TSS	Primary T cells fromperipheralblood	blood
24	chr6:76308400-76308800	Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr6:76308400-76308800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr6:76308400-76308800	Active TSS	Rectal Smooth Muscle	rectum
27	chr6:76308400-76309000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:76308400-76309000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr6:76308400-76309000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:76308400-76309000	Active TSS	Brain Anterior Caudate	brain
31	chr6:76308400-76309000	Active TSS	Colon Smooth Muscle	Colon
32	chr6:76308400-76309000	Active TSS	Rectal Mucosa Donor 29	rectum

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