Variant report

Variant	rs269856
Chromosome Location	chr15:45405463-45405464
allele	G/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	CTBP2	chr15:45404577-45407347	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr15:45405420-45405570	WERI-Rb-1	eye:	n/a	n/a
3	SUZ12	chr15:45403640-45410696	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr15:45405420-45405570	SK-N-SH_RA	brain:	n/a	n/a
5	SUZ12	chr15:45404094-45407411	NT2-D1	testis:	n/a	n/a
6	CTCF	chr15:45405440-45405590	HMEC	breast:	n/a	n/a

Variant related genes	Relation type
DUOXA2	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10851420	0.92[MEX][hapmap]
rs175088	0.82[CHD][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs1898298	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1961660	0.83[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs199138	0.92[MEX][hapmap]
rs2001616	0.83[EUR][1000 genomes]
rs2252371	1.00[MEX][hapmap];0.92[TSI][hapmap]
rs2252479	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2576091	0.87[EUR][1000 genomes]
rs2576092	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs269859	0.92[MEX][hapmap];0.82[TSI][hapmap]
rs269862	1.00[MEX][hapmap];0.82[TSI][hapmap]
rs269868	1.00[MEX][hapmap]
rs4774519	0.85[EUR][1000 genomes]
rs751151	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
12	esv3345210	chr15:45402360-45405508	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs269856	CTD-2651B20.3	cis	Artery Tibial	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45403800-45406800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
2	chr15:45403800-45407000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
3	chr15:45403800-45407000	Enhancers	Pancreas	Pancrea
4	chr15:45404000-45405600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
5	chr15:45404000-45405600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
6	chr15:45404000-45405600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr15:45404000-45405600	Bivalent Enhancer	Fetal Stomach	stomach
8	chr15:45404000-45405600	Bivalent Enhancer	Spleen	Spleen
9	chr15:45404000-45405800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:45404000-45405800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr15:45404000-45405800	Bivalent Enhancer	Fetal Intestine Large	intestine
12	chr15:45404000-45406400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
13	chr15:45404000-45406800	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr15:45404000-45407200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr15:45404200-45405600	Bivalent/Poised TSS	Small Intestine	intestine
16	chr15:45404200-45405800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:45404200-45407000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:45404200-45407200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
19	chr15:45404400-45405600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:45404400-45405800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:45404400-45405800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
22	chr15:45404400-45406400	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
23	chr15:45404400-45406600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
24	chr15:45404400-45407200	Bivalent Enhancer	Fetal Brain Male	brain
25	chr15:45404600-45405600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr15:45404600-45405600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:45404600-45405600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:45404600-45405600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
29	chr15:45404600-45405600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr15:45404600-45405600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:45404600-45405600	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
32	chr15:45404600-45405800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr15:45404600-45405800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
34	chr15:45404600-45406400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
35	chr15:45404800-45407000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr15:45404800-45407800	Bivalent Enhancer	Fetal Heart	heart
37	chr15:45405000-45405600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr15:45405000-45406400	Bivalent Enhancer	Primary B cells from cord blood	blood
39	chr15:45405000-45406800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
40	chr15:45405000-45407000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
41	chr15:45405000-45407200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
42	chr15:45405000-45407400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
43	chr15:45405200-45405800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:45405200-45405800	Flanking Active TSS	Gastric	stomach
45	chr15:45405200-45405800	Bivalent Enhancer	Stomach Mucosa	stomach
46	chr15:45405200-45406200	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
47	chr15:45405200-45406600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr15:45405200-45406800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
49	chr15:45405200-45407000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr15:45405200-45407000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin

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