Variant report

Variant	rs2576089
Chromosome Location	chr15:45406427-45406428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

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	POU2F2	chr15:45406223-45406580	GM12891	blood:	n/a	n/a
3	SUZ12	chr15:45403640-45410696	H1-hESC	embryonic stem cell:	n/a	n/a
4	SUZ12	chr15:45404094-45407411	NT2-D1	testis:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:45406402-45406452	K562	blood:	n/a
2	chr15:45406402-45406452	GM19239	blood:	n/a
3	chr15:45406402-45406452	HPAEpiC	pulmonary alveolar:	n/a
4	chr15:45406402-45406452	U87	brain:	n/a
5	chr15:45406402-45406452	HAEpiC	amniotic membrane:	n/a
6	chr15:45406402-45406452	GM06990	blood:	n/a
7	chr15:45406402-45406452	HEEpiC	esophagus:	n/a
8	chr15:45406402-45406452	SK-N-SH_RA	brain:	n/a
9	chr15:45406402-45406452	A549	lung:	n/a
10	chr15:45406402-45406452	LNCaP	prostate:	n/a
11	chr15:45406402-45406452	SAEC	small airway:	n/a
12	chr15:45406402-45406452	NHBE	bronchial:	n/a
13	chr15:45406402-45406452	ECC-1	luminal epithelium:	n/a
14	chr15:45406402-45406452	HMEC	breast:	n/a
15	chr15:45406402-45406452	HCPEpiC	choroid plexus:	n/a
16	chr15:45406402-45406452	SK-N-MC	brain:	n/a
17	chr15:45406402-45406452	GM12891	blood:	n/a
18	chr15:45406402-45406452	AG09309	skin:	n/a
19	chr15:45406402-45406452	H1-hESC	embryonic stem cell:	embryo
20	chr15:45406402-45406452	PANC-1	pancreas:	n/a
21	chr15:45406402-45406452	HRPEpiC	eye:	n/a
22	chr15:45406402-45406452	RPTEC	kidney:	n/a
23	chr15:45406402-45406452	AG09319	gingival:	n/a
24	chr15:45406402-45406452	MCF-7	breast:	n/a
25	chr15:45406402-45406452	HCT-116	colon:	n/a
26	chr15:45406402-45406452	SKMC	muscle:	n/a
27	chr15:45406402-45406452	GM12878	blood:	n/a
28	chr15:45406402-45406452	HEK293	kidney:	embryo
29	chr15:45406402-45406452	NHDF-neo	bronchial:	n/a
30	chr15:45406402-45406452	HCM	heart:	n/a
31	chr15:45406402-45406452	HIPEpiC	eye:	n/a
32	chr15:45406402-45406452	Caco-2	colon:	n/a
33	chr15:45406402-45406452	AG04449	skin:	fetal
34	chr15:45406402-45406452	AG04450	lung:	fetal
35	chr15:45406402-45406452	MCF10A-Er-Src	breast:	n/a
36	chr15:45406402-45406452	Hela-S3	cervix:	n/a
37	chr15:45406402-45406452	CMK	blood:	n/a
38	chr15:45406402-45406452	PFSK-1	brain:	n/a
39	chr15:45406402-45406452	HRE	kidney:	n/a
40	chr15:45406402-45406452	Jurkat	blood:	n/a
41	chr15:45406402-45406452	NH-A	brain:	n/a
42	chr15:45406402-45406452	BE2_C	brain:	n/a
43	chr15:45406402-45406452	IMR90	lung:	fetal
44	chr15:45406402-45406452	ProgFib	skin:	n/a
45	chr15:45406402-45406452	GM12892	blood:	n/a
46	chr15:45406402-45406452	SK-N-SH	brain:	n/a
47	chr15:45406402-45406452	PrEC	prostate:	n/a
48	chr15:45406402-45406452	HRCEpiC	kidney:	n/a
49	chr15:45406402-45406452	HNPCEpiC	eye:	n/a
50	chr15:45406402-45406452	AoSMC	blood vessel:	n/a

No data

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

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]
rs269855	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
rs2576089	SLC30A4	cis	lymphoblastoid	seeQTL

Chromatin state (count:89 , 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	chr15:45404000-45406800	Bivalent Enhancer	Fetal Muscle Leg	muscle
5	chr15:45404000-45407200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
6	chr15:45404200-45407000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
7	chr15:45404200-45407200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
8	chr15:45404400-45406600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
9	chr15:45404400-45407200	Bivalent Enhancer	Fetal Brain Male	brain
10	chr15:45404800-45407000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:45404800-45407800	Bivalent Enhancer	Fetal Heart	heart
12	chr15:45405000-45406800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
13	chr15:45405000-45407000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:45405000-45407200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
15	chr15:45405000-45407400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
16	chr15:45405200-45406600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr15:45405200-45406800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
18	chr15:45405200-45407000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:45405200-45407000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:45405200-45407200	Bivalent Enhancer	Brain Substantia Nigra	brain
21	chr15:45405400-45406600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:45405400-45406600	Bivalent Enhancer	Brain Cingulate Gyrus	brain
23	chr15:45405400-45406600	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:45405400-45406600	Weak transcription	Right Atrium	heart
25	chr15:45405400-45406600	Bivalent Enhancer	HMEC	breast
26	chr15:45405400-45406800	Bivalent Enhancer	Brain Germinal Matrix	brain
27	chr15:45405400-45406800	Bivalent Enhancer	Fetal Brain Female	brain
28	chr15:45405400-45407000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
29	chr15:45405600-45406600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
30	chr15:45405600-45406600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
31	chr15:45405600-45406800	Enhancers	Spleen	Spleen
32	chr15:45405600-45407000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
33	chr15:45405600-45407000	Bivalent Enhancer	Brain Anterior Caudate	brain
34	chr15:45405600-45407400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:45405800-45406600	Bivalent Enhancer	Brain Angular Gyrus	brain
36	chr15:45405800-45406600	Bivalent Enhancer	Brain Hippocampus Middle	brain
37	chr15:45405800-45406600	Enhancers	Gastric	stomach
38	chr15:45405800-45407000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
39	chr15:45406000-45406600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:45406000-45407000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
41	chr15:45406000-45407000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:45406000-45410800	Bivalent Enhancer	Stomach Mucosa	stomach
43	chr15:45406200-45406600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:45406200-45406600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
45	chr15:45406200-45406800	Bivalent Enhancer	GM12878-XiMat	blood
46	chr15:45406200-45407000	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:45406200-45407000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
48	chr15:45406200-45407000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:45406200-45407000	Flanking Bivalent TSS/Enh	HepG2	liver
50	chr15:45406200-45407000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood

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