Variant report

Variant	rs13015478
Chromosome Location	chr2:113999736-113999737
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	POLR2A	chr2:113998335-114000919	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr2:113997003-114000128	IMR90	lung:	n/a	n/a
3	POLR2A	chr2:113998495-113999803	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr2:113996944-114000866	K562	blood:	n/a	n/a
5	POLR2A	chr2:113999302-114000351	GM12878	blood:	n/a	n/a
6	MAX	chr2:113996927-113999829	A549	lung:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
7	POLR2A	chr2:113999028-113999775	HCT-116	colon:	n/a	n/a
8	CEBPB	chr2:113997572-113999797	HCT-116	colon:	n/a	chr2:113998825-113998836
9	FOSL1	chr2:113997637-113999745	HCT-116	colon:	n/a	chr2:113999384-113999396 chr2:113999387-113999398 chr2:113999385-113999395 chr2:113999385-113999395 chr2:113999386-113999394
10	POLR2A	chr2:113998349-114000010	K562	blood:	n/a	n/a
11	SP1	chr2:113997449-113999766	HCT-116	colon:	n/a	n/a
12	POLR2A	chr2:113997148-113999795	U87	brain:	n/a	n/a
13	SP1	chr2:113997517-113999763	HCT-116	colon:	n/a	n/a
14	MAX	chr2:113997190-113999788	A549	lung:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
15	USF1	chr2:113999135-113999771	HCT-116	colon:	n/a	n/a
16	MAX	chr2:113997553-113999839	HCT-116	colon:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
17	POLR2A	chr2:113998357-114000456	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr2:113997531-114000147	K562	blood:	n/a	n/a
19	MAZ	chr2:113996918-113999877	IMR90	lung:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
20	MAX	chr2:113997526-113999827	HCT-116	colon:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113950220..113951864-chr2:113997428..113999954,2	K562	blood:
2	chr2:113954862..113956783-chr2:113998620..114001129,2	MCF-7	breast:

Variant related genes	Relation type
PAX8	TF binding region
ENSG00000125637	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11886472	0.86[YRI][hapmap]
rs12998725	0.90[CEU][hapmap]
rs1491584	0.82[CEU][hapmap];0.92[MKK][hapmap];0.87[YRI][hapmap]
rs1491586	0.82[CEU][hapmap];0.91[MKK][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2018348	1.00[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35129549	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs35920363	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4849186	0.90[CEU][hapmap]
rs4849187	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459008	chr2:113972945-114010791	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv582713	chr2:113972945-114010791	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv508162	chr2:113983043-114099966	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs13015478	PAX8	cis	Adipose Subcutaneous	GTEx
rs13015478	AC016683.6	cis	Nerve Tibial	GTEx
rs13015478	AC016683.6	cis	lung	GTEx
rs13015478	PAX8	cis	lung	GTEx
rs13015478	PAX8	cis	Whole Blood	GTEx
rs13015478	PAX8	cis	parietal	SCAN
rs13015478	PAX8	cis	Esophagus Muscularis	GTEx
rs13015478	AC016683.6	cis	Artery Tibial	GTEx
rs13015478	LOC654433	cis	parietal	SCAN
rs13015478	AC016683.6	cis	Esophagus Mucosa	GTEx
rs13015478	AC016683.6	cis	Esophagus Muscularis	GTEx
rs13015478	PAX8	cis	Esophagus Mucosa	GTEx
rs13015478	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs13015478	AC016683.6	cis	Muscle Skeletal	GTEx
rs13015478	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs13015478	PAX8	cis	lymphoblastoid	seeQTL
rs13015478	AC016683.6	cis	Skin Sun Exposed Lower leg	GTEx
rs13015478	AC016683.6	cis	Whole Blood	GTEx
rs13015478	LOC654433	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113993400-114000000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:113993400-114006600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr2:113994200-114002000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:113994200-114006600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:113994600-114000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:113994800-114006600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr2:113995000-114006800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:113995200-114000000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr2:113995200-114007000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:113995600-114000200	Weak transcription	Dnd41	blood
11	chr2:113995600-114008600	Weak transcription	GM12878-XiMat	blood
12	chr2:113996600-114000200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:113997000-114000000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:113997000-114000000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr2:113997000-114000000	Enhancers	Placenta Amnion	Placenta Amnion
16	chr2:113997000-114000600	Enhancers	Esophagus	oesophagus
17	chr2:113997400-113999800	Enhancers	Right Ventricle	heart
18	chr2:113997400-114000200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr2:113997600-113999800	Enhancers	Fetal Intestine Large	intestine
20	chr2:113997600-114001000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr2:113998000-113999800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:113998000-113999800	Enhancers	Lung	lung
23	chr2:113998200-114000200	Enhancers	Adipose Nuclei	Adipose
24	chr2:113998200-114000200	Enhancers	HMEC	breast
25	chr2:113998200-114000800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:113998200-114006600	Weak transcription	Fetal Thymus	thymus
27	chr2:113998200-114020600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr2:113998400-113999800	Enhancers	NH-A	brain
29	chr2:113998400-114000000	Enhancers	HSMM	muscle
30	chr2:113998600-113999800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr2:113998600-113999800	Enhancers	NHLF	lung
32	chr2:113998600-114000000	Enhancers	Muscle Satellite Cultured Cells	--
33	chr2:113998600-114000200	Enhancers	Fetal Heart	heart
34	chr2:113998600-114000200	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr2:113998600-114000200	Enhancers	NHDF-Ad	bronchial
36	chr2:113998600-114000200	Enhancers	NHEK	skin
37	chr2:113998600-114000800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:113998800-114000000	Strong transcription	Fetal Kidney	kidney
39	chr2:113998800-114000800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:113998800-114001400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:113998800-114001600	Weak transcription	Fetal Intestine Small	intestine
42	chr2:113998800-114002200	Weak transcription	Liver	Liver
43	chr2:113999000-114000200	Enhancers	A549	lung
44	chr2:113999000-114000800	Enhancers	HepG2	liver
45	chr2:113999000-114001400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:113999000-114001600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr2:113999000-114001800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:113999000-114003000	Weak transcription	Fetal Lung	lung
49	chr2:113999000-114014800	Weak transcription	Colon Smooth Muscle	Colon
50	chr2:113999200-114000000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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