Variant report

Variant	rs2252479
Chromosome Location	chr15:45409013-45409014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr15:45408703-45409183	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr15:45408940-45409090	AG04450	lung:	n/a	n/a
3	MYC	chr15:45408805-45409129	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTBP2	chr15:45408486-45409537	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr15:45408692-45409191	H1-hESC	embryonic stem cell:	n/a	n/a
6	SUZ12	chr15:45403640-45410696	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr15:45408529-45409639	H1-hESC	embryonic stem cell:	n/a	chr15:45408609-45408623
8	BACH1	chr15:45408630-45409090	H1-hESC	embryonic stem cell:	n/a	n/a
9	E2F6	chr15:45408678-45409209	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:45402965..45405384-chr15:45407818..45410560,2	K562	blood:
2	chr15:45407575..45409990-chr15:45413703..45415541,2	K562	blood:
3	chr15:45402172..45404057-chr15:45407808..45410481,2	MCF-7	breast:

No data

Variant related genes	Relation type
DUOX2	TF binding region
ENSG00000140254	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs16977681	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs175088	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1863469	1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1898298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2001616	0.89[AMR][1000 genomes]
rs2252371	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2576091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2576092	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs269856	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4774518	0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4774519	1.00[CHB][hapmap];0.96[EUR][1000 genomes]
rs61751061	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs955152	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS 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	95 gene(s)	inside rSNPs	diseases
2	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
4	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
5	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv457124	chr15:45381998-45460422	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv569312	chr15:45381998-45460422	Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	esv1823029	chr15:45387102-45482245	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv904185	chr15:45394406-45428390	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv904186	chr15:45394406-45434493	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45406000-45410800	Bivalent Enhancer	Stomach Mucosa	stomach
2	chr15:45406600-45410200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:45406600-45410400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr15:45408000-45410200	Bivalent Enhancer	Lung	lung
5	chr15:45408200-45410400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
6	chr15:45408400-45409200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
7	chr15:45408400-45409200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr15:45408400-45409200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
9	chr15:45408400-45410200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
10	chr15:45408400-45410600	Bivalent Enhancer	Fetal Brain Male	brain
11	chr15:45408600-45409200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
12	chr15:45408600-45409200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
13	chr15:45408600-45409200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:45408600-45409200	Bivalent Enhancer	Esophagus	oesophagus
15	chr15:45408600-45409600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
16	chr15:45408600-45409600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:45408600-45409600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
18	chr15:45408600-45409600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
19	chr15:45408600-45409800	Bivalent Enhancer	Fetal Heart	heart
20	chr15:45408600-45410000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
21	chr15:45408600-45410000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:45408600-45410000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
23	chr15:45408600-45410000	Bivalent Enhancer	Fetal Stomach	stomach
24	chr15:45408600-45410000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
25	chr15:45408600-45410200	Bivalent Enhancer	Fetal Muscle Leg	muscle
26	chr15:45408600-45410400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
27	chr15:45408600-45410400	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
28	chr15:45408800-45409200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
29	chr15:45408800-45409200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
30	chr15:45408800-45409200	Bivalent Enhancer	Brain Angular Gyrus	brain
31	chr15:45408800-45409200	Enhancers	Ovary	ovary
32	chr15:45408800-45409200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
33	chr15:45408800-45409200	Bivalent/Poised TSS	NHEK	skin
34	chr15:45408800-45409400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
35	chr15:45408800-45409400	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
36	chr15:45408800-45409400	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain
37	chr15:45408800-45409600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
38	chr15:45408800-45409600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:45408800-45409600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:45408800-45409600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
41	chr15:45408800-45409600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
42	chr15:45408800-45409600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
43	chr15:45408800-45409600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
44	chr15:45408800-45409600	Bivalent Enhancer	Thymus	Thymus
45	chr15:45408800-45409800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
46	chr15:45408800-45409800	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
47	chr15:45408800-45410000	Bivalent Enhancer	HUVEC	blood vessel
48	chr15:45408800-45410200	Bivalent/Poised TSS	Colonic Mucosa	Colon
49	chr15:45408800-45410200	Bivalent Enhancer	Fetal Lung	lung
50	chr15:45408800-45410200	Enhancers	Pancreas	Pancrea

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