Variant report

Variant	rs28366017
Chromosome Location	chr11:46616029-46616030
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:82)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:82 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr11:46615488-46616197	MCF10A-Er-Src	breast:	n/a	n/a
2	MYBL2	chr11:46615327-46616501	HepG2	liver:	n/a	n/a
3	CHD2	chr11:46614792-46616037	GM12878	blood:	n/a	n/a
4	FOS	chr11:46615531-46616209	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr11:46614960-46616164	GM12878	blood:	n/a	n/a
6	POLR2A	chr11:46614530-46616301	HepG2	liver:	n/a	n/a
7	SRF	chr11:46615129-46616124	HCT-116	colon:	n/a	n/a
8	POLR2A	chr11:46615223-46616262	GM12892	blood:	n/a	n/a
9	MTA3	chr11:46615441-46616151	GM12878	blood:	n/a	n/a
10	TBL1XR1	chr11:46615094-46616058	GM12878	blood:	n/a	n/a
11	CUX1	chr11:46615467-46616373	K562	blood:	n/a	n/a
12	GTF2F1	chr11:46615430-46616134	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr11:46615326-46616126	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr11:46615251-46616529	HepG2	liver:	n/a	n/a
15	NFIC	chr11:46615237-46616121	GM12878	blood:	n/a	n/a
16	POLR2A	chr11:46614711-46616058	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr11:46614672-46616062	GM12892	blood:	n/a	n/a
18	MTA3	chr11:46614678-46616317	GM12878	blood:	n/a	n/a
19	HEY1	chr11:46615161-46616666	HepG2	liver:	n/a	chr11:46615536-46615551 chr11:46615494-46615509
20	MXI1	chr11:46615346-46616122	Hela-S3	cervix:	n/a	n/a
21	HCFC1	chr11:46614269-46616394	Hela-S3	cervix:	n/a	n/a
22	ZMIZ1	chr11:46615419-46616177	K562	blood:	n/a	n/a
23	MXI1	chr11:46615022-46616201	GM12878	blood:	n/a	n/a
24	POLR2A	chr11:46614973-46616091	SK-N-MC	brain:	n/a	n/a
25	PML	chr11:46615282-46616149	K562	blood:	n/a	n/a
26	MAX	chr11:46615211-46616033	MCF-7	breast:	n/a	n/a
27	REST	chr11:46615254-46616038	HL-60	blood:	n/a	n/a
28	CUX1	chr11:46615417-46616070	GM12878	blood:	n/a	n/a
29	PML	chr11:46614701-46616481	GM12878	blood:	n/a	n/a
30	MBD4	chr11:46615378-46616043	HepG2	liver:	n/a	n/a
31	MYBL2	chr11:46615194-46616557	HepG2	liver:	n/a	n/a
32	SRF	chr11:46615159-46616033	HCT-116	colon:	n/a	n/a
33	RFX5	chr11:46615117-46616054	Hela-S3	cervix:	n/a	chr11:46615176-46615185
34	TBP	chr11:46615126-46616069	HepG2	liver:	n/a	n/a
35	POLR2A	chr11:46614468-46616236	GM12891	blood:	n/a	n/a
36	MAFF	chr11:46615564-46616260	K562	blood:	n/a	n/a
37	RFX5	chr11:46615573-46616370	K562	blood:	n/a	n/a
38	STAT3	chr11:46615810-46616054	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr11:46615208-46616065	HL-60	blood:	n/a	n/a
40	TEAD4	chr11:46615503-46616078	HepG2	liver:	n/a	n/a
41	POLR2A	chr11:46615330-46616155	HepG2	liver:	n/a	n/a
42	RCOR1	chr11:46615454-46616179	GM12878	blood:	n/a	n/a
43	MAFK	chr11:46615498-46616317	HepG2	liver:	n/a	n/a
44	SRF	chr11:46615095-46616076	MCF-7	breast:	n/a	n/a
45	EP300	chr11:46615371-46616243	HepG2	liver:	n/a	chr11:46616149-46616163 chr11:46615537-46615546 chr11:46615541-46615550 chr11:46615538-46615547
46	NR2F2	chr11:46615242-46616276	K562	blood:	n/a	n/a
47	RUNX3	chr11:46614909-46616273	GM12878	blood:	n/a	n/a
48	RELA	chr11:46615044-46616197	GM10847	blood:	n/a	n/a
49	MAZ	chr11:46614958-46616151	GM12878	blood:	n/a	n/a
50	MBD4	chr11:46615334-46616246	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:46612073..46617371-chr11:46634890..46640526,10	MCF-7	breast:
2	chr11:46615628..46616226-chr3:101405144..101405659,2	Hela-S3	cervix:
3	chr11:46610656..46614165-chr11:46614345..46616475,3	MCF-7	breast:
4	chr11:46615111..46616180-chr11:46638190..46639491,4	MCF-7	breast:
5	chr11:46612682..46616459-chr11:46637148..46640033,6	MCF-7	breast:
6	chr11:46613853..46617362-chr11:46635690..46640935,4	K562	blood:
7	chr11:46607617..46609574-chr11:46615732..46617530,2	K562	blood:
8	chr11:46615828..46618723-chr11:46623261..46625770,2	MCF-7	breast:

No data

Variant related genes	Relation type
AMBRA1	TF binding region
ENSG00000180423	Chromatin interaction
ENSG00000114391	Chromatin interaction
ENSG00000175224	Chromatin interaction
ENSG00000110497	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11038965	1.00[MEX][hapmap]
rs3136452	1.00[MEX][hapmap]
rs3740976	0.89[ASN][1000 genomes]
rs4474394	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs72910085	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044225	chr11:46472580-46771102	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv541030	chr11:46472580-46771102	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046990	chr11:46501436-46669636	Active TSS Weak transcription Strong transcription Enhancers 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	18 gene(s)	inside rSNPs	diseases
4	nsv541031	chr11:46501436-46669636	Flanking Active TSS Enhancers Weak transcription Strong transcription 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	18 gene(s)	inside rSNPs	diseases
5	nsv897321	chr11:46515902-46673344	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46612200-46616200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:46613800-46616200	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr11:46613800-46616200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr11:46613800-46616400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr11:46614000-46616400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:46614200-46616200	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr11:46614200-46616200	Active TSS	Ovary	ovary
8	chr11:46614200-46616200	Active TSS	Right Atrium	heart
9	chr11:46614200-46616200	Active TSS	HSMM	muscle
10	chr11:46614200-46616400	Active TSS	A549	lung
11	chr11:46614600-46616200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:46614600-46616200	Active TSS	Fetal Muscle Trunk	muscle
13	chr11:46614600-46616200	Active TSS	Psoas Muscle	Psoas
14	chr11:46614600-46616400	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr11:46614600-46616400	Active TSS	Fetal Kidney	kidney
16	chr11:46614600-46616400	Bivalent/Poised TSS	HepG2	liver
17	chr11:46614800-46616200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr11:46614800-46616200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:46614800-46616400	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr11:46614800-46616400	Active TSS	Stomach Smooth Muscle	stomach
21	chr11:46615000-46616200	Active TSS	Brain Germinal Matrix	brain
22	chr11:46615000-46616200	Active TSS	NH-A	brain
23	chr11:46615000-46616400	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr11:46615000-46616600	Active TSS	Colonic Mucosa	Colon
25	chr11:46615400-46616200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr11:46615600-46616200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr11:46615600-46616400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr11:46615600-46616400	Enhancers	Stomach Mucosa	stomach
29	chr11:46615600-46618600	Weak transcription	Small Intestine	intestine
30	chr11:46615600-46618800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr11:46615600-46625000	Weak transcription	Gastric	stomach
32	chr11:46615600-46636800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:46615800-46616200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:46615800-46616200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr11:46615800-46616200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr11:46615800-46616200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr11:46615800-46616200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
38	chr11:46615800-46616200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr11:46615800-46616200	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr11:46615800-46616200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr11:46615800-46616200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr11:46615800-46616200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr11:46615800-46616200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr11:46615800-46616200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr11:46615800-46616200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr11:46615800-46616200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr11:46615800-46616200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr11:46615800-46616200	Flanking Active TSS	Brain Angular Gyrus	brain
49	chr11:46615800-46616200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
50	chr11:46615800-46616200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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