Variant report

Variant	rs269855
Chromosome Location	chr15:45405987-45405988
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	CTBP2	chr15:45404577-45407347	H1-hESC	embryonic stem cell:	n/a	n/a
2	SUZ12	chr15:45403640-45410696	H1-hESC	embryonic stem cell:	n/a	n/a
3	SUZ12	chr15:45404094-45407411	NT2-D1	testis:	n/a	n/a

Variant related genes	Relation type
DUOX2	TF binding region
DUOXA2	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1370114	1.00[AMR][1000 genomes]
rs182090	1.00[AMR][1000 genomes]
rs199137	1.00[AMR][1000 genomes]
rs2412956	1.00[AMR][1000 genomes]
rs2576089	1.00[ASW][hapmap];0.88[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs269865	1.00[AMR][1000 genomes]
rs269867	1.00[AMR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs269855	SLC30A4	cis	lymphoblastoid	seeQTL

Chromatin state (count:65 , 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	chr15:45404000-45406400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
5	chr15:45404000-45406800	Bivalent Enhancer	Fetal Muscle Leg	muscle
6	chr15:45404000-45407200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
7	chr15:45404200-45407000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
8	chr15:45404200-45407200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
9	chr15:45404400-45406400	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
10	chr15:45404400-45406600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
11	chr15:45404400-45407200	Bivalent Enhancer	Fetal Brain Male	brain
12	chr15:45404600-45406400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr15:45404800-45407000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr15:45404800-45407800	Bivalent Enhancer	Fetal Heart	heart
15	chr15:45405000-45406400	Bivalent Enhancer	Primary B cells from cord blood	blood
16	chr15:45405000-45406800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
17	chr15:45405000-45407000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:45405000-45407200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
19	chr15:45405000-45407400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
20	chr15:45405200-45406200	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
21	chr15:45405200-45406600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr15:45405200-45406800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
23	chr15:45405200-45407000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:45405200-45407000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:45405200-45407200	Bivalent Enhancer	Brain Substantia Nigra	brain
26	chr15:45405400-45406200	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
27	chr15:45405400-45406400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
28	chr15:45405400-45406400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
29	chr15:45405400-45406400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:45405400-45406400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:45405400-45406400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
32	chr15:45405400-45406400	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
33	chr15:45405400-45406400	Bivalent Enhancer	Right Ventricle	heart
34	chr15:45405400-45406400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
35	chr15:45405400-45406600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:45405400-45406600	Bivalent Enhancer	Brain Cingulate Gyrus	brain
37	chr15:45405400-45406600	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:45405400-45406600	Weak transcription	Right Atrium	heart
39	chr15:45405400-45406600	Bivalent Enhancer	HMEC	breast
40	chr15:45405400-45406800	Bivalent Enhancer	Brain Germinal Matrix	brain
41	chr15:45405400-45406800	Bivalent Enhancer	Fetal Brain Female	brain
42	chr15:45405400-45407000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
43	chr15:45405600-45406000	Bivalent Enhancer	Small Intestine	intestine
44	chr15:45405600-45406400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:45405600-45406400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
46	chr15:45405600-45406600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
47	chr15:45405600-45406600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
48	chr15:45405600-45406800	Enhancers	Spleen	Spleen
49	chr15:45405600-45407000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
50	chr15:45405600-45407000	Bivalent Enhancer	Brain Anterior Caudate	brain

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