Variant report

Variant	rs11249653
Chromosome Location	chr5:179104757-179104758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179104629-179106368	GM12892	blood:	n/a	n/a
2	POLR2A	chr5:179104608-179106366	PANC-1	pancreas:	n/a	n/a
3	JUN	chr5:179104730-179105981	K562	blood:	n/a	chr5:179105577-179105590
4	POLR2A	chr5:179101513-179106171	HepG2	liver:	n/a	n/a
5	MYC	chr5:179104701-179106303	K562	blood:	n/a	n/a
6	POLR2A	chr5:179104685-179105934	K562	blood:	n/a	n/a
7	ELF1	chr5:179104757-179106582	MCF-7	breast:	n/a	chr5:179104874-179104887
8	ELF1	chr5:179104754-179104959	K562	blood:	n/a	chr5:179104874-179104887
9	RCOR1	chr5:179104734-179106442	IMR90	lung:	n/a	n/a
10	PAX5	chr5:179104448-179104758	GM12878	blood:	n/a	n/a
11	PAX5	chr5:179104380-179104798	GM12878	blood:	n/a	n/a
12	MAX	chr5:179104755-179106540	A549	lung:	n/a	n/a
13	HEY1	chr5:179104484-179105826	K562	blood:	n/a	n/a
14	POLR2A	chr5:179104750-179105823	K562	blood:	n/a	n/a
15	PAX5	chr5:179104471-179104783	GM12892	blood:	n/a	n/a
16	MAX	chr5:179104727-179106535	MCF-7	breast:	n/a	n/a
17	POLR2A	chr5:179104545-179106632	K562	blood:	n/a	n/a
18	MAX	chr5:179104723-179106265	HepG2	liver:	n/a	n/a
19	ELF1	chr5:179104387-179104997	GM12878	blood:	n/a	chr5:179104874-179104887
20	RUNX3	chr5:179104739-179105006	GM12878	blood:	n/a	n/a
21	PAX5	chr5:179104307-179104835	GM12878	blood:	n/a	n/a
22	MAX	chr5:179104702-179106433	K562	blood:	n/a	n/a
23	ZNF263	chr5:179104670-179106633	HEK293-T-REx	kidney:	n/a	chr5:179106497-179106506
24	POLR2A	chr5:179104558-179105989	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr5:179104507-179106685	GM12878	blood:	n/a	n/a
26	POLR2A	chr5:179104708-179105859	GM12892	blood:	n/a	n/a
27	POLR2A	chr5:179104621-179105956	PFSK-1	brain:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179101962..179108661-chr5:179122383..179128408,19	MCF-7	breast:
2	chr5:179104081..179106481-chr5:179247871..179249548,2	K562	blood:
3	chr5:179100838..179108153-chr5:179124449..179130181,22	K562	blood:
4	chr5:179049533..179052334-chr5:179104256..179107492,4	MCF-7	breast:
5	chr5:179104047..179107935-chr5:179157751..179161258,3	K562	blood:
6	chr5:179104105..179106791-chr5:179194829..179197317,2	K562	blood:
7	chr5:179101603..179111989-chr5:179122927..179129527,32	MCF-7	breast:
8	chr5:179100989..179111182-chr5:179122076..179128627,19	K562	blood:
9	chr5:179047581..179051358-chr5:179102429..179108878,16	K562	blood:
10	chr5:179102368..179107935-chr5:179157286..179161555,5	K562	blood:
11	chr5:179104067..179106595-chr5:179220718..179223236,3	MCF-7	breast:
12	chr5:179048811..179053260-chr5:179101652..179108160,8	MCF-7	breast:
13	chr5:179104088..179107429-chr5:179222108..179224529,3	MCF-7	breast:
14	chr5:179048156..179052144-chr5:179103013..179109071,12	K562	blood:
15	chr5:178986726..178988892-chr5:179104044..179106638,2	K562	blood:
16	chr5:179032616..179037685-chr5:179101606..179106447,5	K562	blood:
17	chr5:179103716..179105834-chr5:179232132..179234075,2	MCF-7	breast:
18	chr5:179102777..179105502-chr5:179129566..179131277,2	MCF-7	breast:

No data

Variant related genes	Relation type
CANX	TF binding region
HMGB3P22	TF binding region
ENSG00000161013	Chromatin interaction
ENSG00000176783	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000213316	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10066644	0.88[ASN][1000 genomes]
rs11249654	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11739941	0.84[ASN][1000 genomes]
rs11747219	0.85[ASN][1000 genomes]
rs13159123	0.84[ASN][1000 genomes]
rs7700649	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic 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 miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv1023502	chr5:179086091-179105316	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179085800-179104800	Weak transcription	Right Ventricle	heart
2	chr5:179085800-179105000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:179086200-179104800	Weak transcription	Brain Angular Gyrus	brain
4	chr5:179091800-179104800	Weak transcription	Ovary	ovary
5	chr5:179091800-179104800	Weak transcription	NHLF	lung
6	chr5:179092200-179105000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:179092600-179104800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr5:179092800-179105000	Weak transcription	Left Ventricle	heart
9	chr5:179093000-179104800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:179093000-179105000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:179093400-179104800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr5:179093600-179104800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr5:179098200-179104800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr5:179102400-179104800	Weak transcription	Fetal Lung	lung
15	chr5:179103400-179104800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:179103600-179104800	Enhancers	Pancreas	Pancrea
17	chr5:179103800-179104800	Enhancers	Primary B cells from peripheral blood	blood
18	chr5:179103800-179104800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr5:179103800-179105600	Active TSS	Hela-S3	cervix
20	chr5:179103800-179106400	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr5:179104000-179104800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr5:179104000-179104800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr5:179104000-179104800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr5:179104000-179105000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr5:179104000-179105000	Enhancers	Fetal Brain Male	brain
26	chr5:179104000-179105000	Flanking Active TSS	Dnd41	blood
27	chr5:179104200-179104800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr5:179104200-179104800	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr5:179104200-179104800	Enhancers	Fetal Thymus	thymus
30	chr5:179104200-179105000	Enhancers	Primary B cells from cord blood	blood
31	chr5:179104200-179105000	Enhancers	Stomach Mucosa	stomach
32	chr5:179104200-179105600	Active TSS	A549	lung
33	chr5:179104200-179105600	Active TSS	K562	blood
34	chr5:179104200-179106600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:179104400-179105000	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr5:179104400-179105000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:179104400-179105000	Enhancers	Brain Cingulate Gyrus	brain
38	chr5:179104400-179105000	Weak transcription	Lung	lung
39	chr5:179104400-179105000	Enhancers	Spleen	Spleen
40	chr5:179104400-179105200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:179104400-179105200	Active TSS	Duodenum Mucosa	Duodenum
42	chr5:179104400-179105400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:179104400-179105600	Active TSS	Muscle Satellite Cultured Cells	--
44	chr5:179104400-179105600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:179104400-179105600	Active TSS	HepG2	liver
46	chr5:179104400-179105800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:179104400-179105800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:179104400-179105800	Active TSS	GM12878-XiMat	blood
49	chr5:179104400-179106400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr5:179104600-179104800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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