Variant report

Variant	rs2001616
Chromosome Location	chr15:45404066-45404067
allele	A/G
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	E2F6	chr15:45403680-45404381	H1-hESC	embryonic stem cell:	n/a	chr15:45404163-45404174 chr15:45403822-45403831 chr15:45403940-45403952 chr15:45404163-45404174 chr15:45404163-45404174 chr15:45404160-45404177 chr15:45403820-45403830 chr15:45404163-45404174
2	SUZ12	chr15:45403640-45410696	H1-hESC	embryonic stem cell:	n/a	n/a
3	ZNF143	chr15:45403913-45404094	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr15:45403982-45404283	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45402965..45405384-chr15:45407818..45410560,2	K562	blood:

Variant related genes	Relation type
DUOXA2	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10851420	0.82[JPT][hapmap]
rs1108085	0.82[JPT][hapmap]
rs166574	0.82[AMR][1000 genomes]
rs175088	0.85[AMR][1000 genomes]
rs1898298	0.85[AMR][1000 genomes]
rs190599	0.83[AMR][1000 genomes]
rs1961660	0.82[JPT][hapmap];0.83[AMR][1000 genomes]
rs199138	0.82[JPT][hapmap]
rs2002813	0.82[JPT][hapmap]
rs2252371	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2252479	0.89[AMR][1000 genomes]
rs2554451	0.82[JPT][hapmap]
rs2576091	0.89[AMR][1000 genomes]
rs2576092	0.89[AMR][1000 genomes]
rs269856	0.83[EUR][1000 genomes]
rs269859	0.82[JPT][hapmap];0.85[AMR][1000 genomes]
rs269862	0.82[JPT][hapmap];0.83[AMR][1000 genomes]
rs269863	0.85[AMR][1000 genomes]
rs269866	0.82[JPT][hapmap]
rs269868	0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs3743222	0.82[JPT][hapmap]
rs4775744	0.82[JPT][hapmap]
rs57659670	0.83[AMR][1000 genomes]
rs7171366	0.82[JPT][hapmap]
rs7180106	0.82[JPT][hapmap]
rs7183046	0.82[JPT][hapmap]
rs73406330	0.81[AMR][1000 genomes]
rs8024922	0.82[JPT][hapmap]
rs953733	0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs955152	0.88[AMR][1000 genomes];0.85[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
rs2001616	CTD-2651B20.3	cis	Artery Tibial	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45381400-45404600	Weak transcription	Right Atrium	heart
2	chr15:45403600-45404200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:45403600-45404200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:45403600-45404600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
5	chr15:45403600-45404600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr15:45403600-45404600	Bivalent Enhancer	Right Ventricle	heart
7	chr15:45403800-45404200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
8	chr15:45403800-45404200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:45403800-45404200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:45403800-45404400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:45403800-45404600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:45403800-45404600	Bivalent Enhancer	Primary B cells from cord blood	blood
13	chr15:45403800-45404600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
14	chr15:45403800-45404600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
15	chr15:45403800-45404600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:45403800-45404600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:45403800-45404600	Bivalent Enhancer	Fetal Heart	heart
18	chr15:45403800-45406800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
19	chr15:45403800-45407000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
20	chr15:45403800-45407000	Enhancers	Pancreas	Pancrea
21	chr15:45404000-45404200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
22	chr15:45404000-45404200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr15:45404000-45404200	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr15:45404000-45404200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
25	chr15:45404000-45404200	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
26	chr15:45404000-45404200	Flanking Active TSS	Gastric	stomach
27	chr15:45404000-45404200	Bivalent Enhancer	Left Ventricle	heart
28	chr15:45404000-45404200	Bivalent Enhancer	Thymus	Thymus
29	chr15:45404000-45404400	Bivalent Enhancer	Brain Hippocampus Middle	brain
30	chr15:45404000-45404400	Bivalent Enhancer	Psoas Muscle	Psoas
31	chr15:45404000-45404400	Bivalent Enhancer	HMEC	breast
32	chr15:45404000-45404600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
33	chr15:45404000-45404600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
34	chr15:45404000-45404600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
35	chr15:45404000-45404600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:45404000-45404600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:45404000-45404600	Bivalent Enhancer	Brain Anterior Caudate	brain
38	chr15:45404000-45404600	Bivalent/Poised TSS	Colonic Mucosa	Colon
39	chr15:45404000-45404600	Bivalent Enhancer	Ovary	ovary
40	chr15:45404000-45405000	Bivalent Enhancer	Stomach Mucosa	stomach
41	chr15:45404000-45405200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
42	chr15:45404000-45405200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
43	chr15:45404000-45405400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
44	chr15:45404000-45405400	Bivalent Enhancer	Fetal Intestine Small	intestine
45	chr15:45404000-45405400	Bivalent Enhancer	Lung	lung
46	chr15:45404000-45405600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
47	chr15:45404000-45405600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
48	chr15:45404000-45405600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
49	chr15:45404000-45405600	Bivalent Enhancer	Fetal Stomach	stomach
50	chr15:45404000-45405600	Bivalent Enhancer	Spleen	Spleen

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