Variant report

Variant	rs3016264
Chromosome Location	chr11:57409628-57409629
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:57406679-57409638	PBDE	blood:	n/a	n/a
2	POLR2A	chr11:57404829-57418710	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr11:57404853-57409799	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr11:57404978-57410762	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr11:57404927-57409727	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr11:57409592-57409692	HepG2	liver:	n/a	n/a
7	POLR2A	chr11:57404802-57417187	SK-N-MC	brain:	n/a	n/a
8	CTCF	chr11:57409500-57409650	HVMF	connective:	n/a	n/a
9	POLR2A	chr11:57405031-57409669	PFSK-1	brain:	n/a	n/a
10	CTCF	chr11:57409520-57409670	HCFaa	heart:	n/a	n/a
11	SMC3	chr11:57408359-57409756	SK-N-SH	brain:	n/a	chr11:57409164-57409178
12	POLR2A	chr11:57408996-57409649	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr11:57408982-57409677	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr11:57404949-57409673	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:57405566..57408530-chr11:57408605..57410550,2	MCF-7	breast:
2	chr11:57335324..57336323-chr11:57408291..57409695,14	MCF-7	breast:
3	chr11:57409445..57411077-chr11:57414128..57416873,2	K562	blood:
4	chr11:57334539..57338384-chr11:57406664..57411574,5	MCF-7	breast:
5	chr11:57224546..57225432-chr11:57408726..57409938,3	K562	blood:
6	chr11:57335355..57336298-chr11:57408531..57409635,7	K562	blood:
7	chr11:57293312..57295959-chr11:57408961..57411007,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000254602	TF binding region
ENSG00000166793	Chromatin interaction
ENSG00000254602	Chromatin interaction
ENSG00000156587	Chromatin interaction
ENSG00000172409	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10160797	1.00[AMR][1000 genomes]
rs12282980	1.00[AMR][1000 genomes]
rs1941721	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2911725	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2926660	0.89[AFR][1000 genomes]
rs2926663	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2956980	0.90[AFR][1000 genomes]
rs2956983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2956984	0.82[AFR][1000 genomes]
rs2969941	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2969942	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2969945	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs3016261	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3016262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3016263	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3016293	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs600251	0.89[AFR][1000 genomes]
rs603420	0.89[AFR][1000 genomes]
rs610801	0.89[AFR][1000 genomes]
rs660400	0.89[AFR][1000 genomes]
rs686303	0.84[AFR][1000 genomes]
rs7127878	1.00[AMR][1000 genomes]
rs7939745	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	esv992553	chr11:57408294-57419351	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57403000-57412200	Weak transcription	Hela-S3	cervix
2	chr11:57407200-57412200	Weak transcription	Ovary	ovary
3	chr11:57407400-57412600	Weak transcription	GM12878-XiMat	blood
4	chr11:57407600-57412200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr11:57407600-57412200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr11:57407600-57412200	Weak transcription	Spleen	Spleen
7	chr11:57407600-57413000	Weak transcription	Right Ventricle	heart
8	chr11:57407600-57413200	Weak transcription	Esophagus	oesophagus
9	chr11:57407800-57412200	Weak transcription	Pancreas	Pancrea
10	chr11:57408000-57412000	Weak transcription	Colon Smooth Muscle	Colon
11	chr11:57408000-57412200	Weak transcription	Lung	lung
12	chr11:57408200-57410600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:57408200-57411200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:57408200-57411200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr11:57408200-57411400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:57408200-57411400	Genic enhancers	Fetal Muscle Leg	muscle
17	chr11:57408200-57412000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:57408200-57412000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr11:57408400-57410600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr11:57408400-57412200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr11:57408600-57410400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:57408600-57411200	Weak transcription	NHEK	skin
23	chr11:57408800-57410200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr11:57408800-57410600	Weak transcription	Placenta	Placenta
25	chr11:57408800-57411600	Genic enhancers	H1 Cell Line	embryonic stem cell
26	chr11:57408800-57411800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr11:57408800-57412000	Weak transcription	Left Ventricle	heart
28	chr11:57408800-57412000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr11:57408800-57412000	Weak transcription	Right Atrium	heart
30	chr11:57408800-57412200	Weak transcription	Adipose Nuclei	Adipose
31	chr11:57408800-57412200	Weak transcription	Brain Hippocampus Middle	brain
32	chr11:57408800-57412200	Weak transcription	Thymus	Thymus
33	chr11:57408800-57412600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr11:57408800-57412600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr11:57408800-57413400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr11:57409000-57409800	Enhancers	Primary hematopoietic stem cells	blood
37	chr11:57409000-57410400	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr11:57409000-57410400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr11:57409000-57410600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
40	chr11:57409000-57411000	Weak transcription	HUVEC	blood vessel
41	chr11:57409000-57411200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr11:57409000-57411200	Weak transcription	K562	blood
43	chr11:57409000-57411400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr11:57409000-57411600	Genic enhancers	HUES48 Cell Line	embryonic stem cell
45	chr11:57409000-57411600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr11:57409000-57412000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr11:57409000-57412000	Weak transcription	Brain Angular Gyrus	brain
48	chr11:57409000-57412000	Weak transcription	Brain Anterior Caudate	brain
49	chr11:57409000-57412000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr11:57409000-57412000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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