Variant report

Variant	rs11239309
Chromosome Location	chr10:45496845-45496846
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	POLR2A	chr10:45496617-45497281	SK-N-SH	brain:	n/a	n/a
2	MAFK	chr10:45496699-45497226	IMR90	lung:	n/a	n/a
3	E2F6	chr10:45496064-45497160	H1-hESC	embryonic stem cell:	n/a	chr10:45496377-45496386 chr10:45496510-45496519
4	MXI1	chr10:45495951-45497346	GM12878	blood:	n/a	n/a
5	EP300	chr10:45496727-45497513	ECC-1	luminal epithelium:	n/a	chr10:45497489-45497497
6	CTCF	chr10:45496740-45496890	BE2_C	brain:	n/a	n/a
7	CTCF	chr10:45496214-45497112	K562	blood:	n/a	chr10:45496982-45496991
8	REST	chr10:45495843-45497400	H1-neurons	neurons:	n/a	chr10:45496513-45496526
9	POLR2A	chr10:45495827-45497469	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr10:45495406-45497436	NB4	blood:	n/a	n/a
11	MYC	chr10:45495915-45497699	K562	blood:	n/a	chr10:45497487-45497496
12	MAX	chr10:45496061-45497181	GM12878	blood:	n/a	n/a
13	CTCF	chr10:45496668-45497083	K562	blood:	n/a	chr10:45496982-45496991
14	POU2F2	chr10:45496776-45497122	GM12878	blood:	n/a	chr10:45496997-45497007 chr10:45496997-45497007 chr10:45496997-45497006 chr10:45496994-45497008
15	TCF12	chr10:45496122-45497380	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr10:45496093-45497123	K562	blood:	n/a	n/a
17	NR3C1	chr10:45496804-45497341	ECC-1	luminal epithelium:	n/a	chr10:45496935-45496961 chr10:45496941-45496955
18	MAX	chr10:45496113-45497240	MCF-7	breast:	n/a	n/a
19	PML	chr10:45495748-45497222	GM12878	blood:	n/a	n/a
20	POLR2A	chr10:45495844-45497237	GM12878	blood:	n/a	n/a
21	POLR2A	chr10:45495910-45497239	GM19099	blood:	n/a	n/a
22	TEAD4	chr10:45496686-45497173	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr10:45496840-45496990	HMEC	breast:	n/a	n/a
24	TAF1	chr10:45496156-45497166	K562	blood:	n/a	n/a
25	TEAD4	chr10:45496659-45497288	K562	blood:	n/a	n/a
26	MAX	chr10:45495507-45497380	NB4	blood:	n/a	n/a
27	IRF1	chr10:45495980-45497148	K562	blood:	n/a	n/a
28	POLR2A	chr10:45496118-45497226	HUVEC	blood vessel:	n/a	n/a
29	SRF	chr10:45496816-45497292	ECC-1	luminal epithelium:	n/a	n/a
30	UBTF	chr10:45496219-45497058	K562	blood:	n/a	n/a
31	POLR2A	chr10:45496009-45497280	GM12892	blood:	n/a	n/a
32	JUND	chr10:45496084-45497532	K562	blood:	n/a	chr10:45496424-45496432
33	MXI1	chr10:45496727-45497452	K562	blood:	n/a	n/a
34	MYC	chr10:45495890-45497166	K562	blood:	n/a	n/a
35	E2F6	chr10:45496136-45496898	A549	lung:	n/a	chr10:45496377-45496386 chr10:45496510-45496519
36	POLR2A	chr10:45495646-45497279	GM12891	blood:	n/a	n/a
37	BHLHE40	chr10:45496779-45497089	K562	blood:	n/a	n/a
38	YY1	chr10:45496845-45497170	GM12891	blood:	n/a	n/a
39	E2F6	chr10:45495633-45497319	K562	blood:	n/a	chr10:45496377-45496386 chr10:45496510-45496519
40	TBL1XR1	chr10:45496273-45497149	K562	blood:	n/a	n/a
41	NFIC	chr10:45496497-45497446	ECC-1	luminal epithelium:	n/a	n/a
42	TBP	chr10:45495932-45497081	H1-hESC	embryonic stem cell:	n/a	n/a
43	MAFK	chr10:45496759-45497242	K562	blood:	n/a	n/a
44	EP300	chr10:45496737-45497414	ECC-1	luminal epithelium:	n/a	n/a
45	CTCF	chr10:45496800-45496950	GM12866	blood:	n/a	n/a
46	POLR2A	chr10:45496558-45497359	GM12892	blood:	n/a	n/a
47	CHD1	chr10:45496807-45496963	H1-hESC	embryonic stem cell:	n/a	n/a
48	MAX	chr10:45495998-45497131	A549	lung:	n/a	n/a
49	POLR2A	chr10:45496114-45497162	GM12891	blood:	n/a	n/a
50	MAX	chr10:45495594-45497260	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:45496607..45498157-chr10:45521070..45522987,2	K562	blood:
2	chr10:45454284..45457608-chr10:45494603..45497438,3	K562	blood:
3	chr10:45454284..45457115-chr10:45494603..45497911,3	K562	blood:
4	chr10:45466696..45473467-chr10:45492241..45499604,15	K562	blood:
5	chr10:45473637..45475496-chr10:45496337..45498041,2	MCF-7	breast:
6	chr10:45496341..45497908-chr10:45904514..45906442,2	K562	blood:
7	chr10:45472874..45475868-chr10:45493532..45497096,3	K562	blood:
8	chr10:45494680..45497168-chr10:45675442..45677371,2	K562	blood:
9	chr10:45474000..45475702-chr10:45494679..45496847,2	MCF-7	breast:
10	chr10:45495745..45498371-chr10:45630285..45633118,2	K562	blood:

Variant related genes	Relation type
C10orf25	TF binding region
ENSG00000273363	Chromatin interaction
ENSG00000165507	Chromatin interaction
ENSG00000226937	Chromatin interaction
ENSG00000227683	Chromatin interaction
ENSG00000224812	Chromatin interaction
ENSG00000107551	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11239299	1.00[AMR][1000 genomes]
rs11239303	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11239305	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11239306	1.00[AMR][1000 genomes]
rs11239307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239308	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239311	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11239315	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11239319	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11239323	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11239324	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11239342	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11239343	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11239345	0.97[EUR][1000 genomes]
rs11239346	0.97[EUR][1000 genomes]
rs12354652	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12358699	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12359377	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12359697	0.94[EUR][1000 genomes]
rs12359954	1.00[AMR][1000 genomes]
rs17157322	0.94[EUR][1000 genomes]
rs35521977	1.00[AMR][1000 genomes]
rs3740092	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3740093	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3758399	1.00[AMR][1000 genomes]
rs3758400	1.00[AMR][1000 genomes]
rs41301599	1.00[AMR][1000 genomes]
rs41301601	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41301609	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41301611	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41306544	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41306546	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59381196	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61269477	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv831848	chr10:45490176-45667670	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45492600-45497800	Enhancers	HepG2	liver
2	chr10:45495600-45497400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr10:45495600-45498000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr10:45495800-45497000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr10:45495800-45497000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr10:45495800-45497200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr10:45495800-45497200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
8	chr10:45495800-45497400	Active TSS	H9 Cell Line	embryonic stem cell
9	chr10:45495800-45497600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr10:45495800-45497600	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr10:45495800-45497800	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr10:45496000-45497000	Active TSS	Liver	Liver
13	chr10:45496000-45497200	Active TSS	Fetal Brain Female	brain
14	chr10:45496000-45497200	Active TSS	Lung	lung
15	chr10:45496000-45497200	Active TSS	Ovary	ovary
16	chr10:45496000-45497200	Active TSS	Rectal Smooth Muscle	rectum
17	chr10:45496000-45497400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr10:45496000-45497400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr10:45496000-45497400	Active TSS	Aorta	Aorta
20	chr10:45496000-45497400	Active TSS	Brain Germinal Matrix	brain
21	chr10:45496000-45497400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr10:45496000-45497400	Active TSS	Fetal Lung	lung
23	chr10:45496000-45497400	Active TSS	Left Ventricle	heart
24	chr10:45496000-45497400	Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr10:45496000-45497600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr10:45496000-45497600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr10:45496000-45497600	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr10:45496000-45497600	Active TSS	Fetal Stomach	stomach
29	chr10:45496000-45497600	Active TSS	Psoas Muscle	Psoas
30	chr10:45496000-45497600	Active TSS	Thymus	Thymus
31	chr10:45496200-45497000	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr10:45496200-45497000	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr10:45496200-45497000	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr10:45496200-45497000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr10:45496200-45497000	Active TSS	Brain Anterior Caudate	brain
36	chr10:45496200-45497000	Active TSS	Duodenum Mucosa	Duodenum
37	chr10:45496200-45497000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr10:45496200-45497000	Active TSS	Stomach Mucosa	stomach
39	chr10:45496200-45497000	Active TSS	NHLF	lung
40	chr10:45496200-45497200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr10:45496200-45497200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr10:45496200-45497200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr10:45496200-45497200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr10:45496200-45497200	Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr10:45496200-45497200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr10:45496200-45497200	Active TSS	Colon Smooth Muscle	Colon
47	chr10:45496200-45497200	Active TSS	Esophagus	oesophagus
48	chr10:45496200-45497200	Active TSS	Fetal Brain Male	brain
49	chr10:45496200-45497200	Active TSS	Spleen	Spleen
50	chr10:45496200-45497200	Active TSS	Dnd41	blood

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