Variant report

Variant	rs7587376
Chromosome Location	chr2:114041434-114041435
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	TEAD4	chr2:114041221-114042062	ECC-1	luminal epithelium:	n/a	n/a
2	EP300	chr2:114040355-114042007	A549	lung:	n/a	chr2:114041601-114041617
3	MAX	chr2:114041248-114041792	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr2:114041150-114041808	A549	lung:	n/a	n/a
5	TEAD4	chr2:114041305-114041893	SK-N-SH	brain:	n/a	n/a
6	PBX3	chr2:114041196-114041930	SK-N-SH	brain:	n/a	n/a
7	FOSL2	chr2:114041260-114041753	SK-N-SH	brain:	n/a	chr2:114041379-114041389 chr2:114041381-114041392 chr2:114041380-114041388
8	MYC	chr2:114041213-114041733	MCF10A-Er-Src	breast:	n/a	n/a
9	EP300	chr2:114040470-114042086	ECC-1	luminal epithelium:	n/a	chr2:114042041-114042048 chr2:114041601-114041617
10	ZNF384	chr2:114040915-114041501	K562	blood:	n/a	n/a
11	ZBTB33	chr2:114041262-114041805	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr2:114040002-114042969	U87	brain:	n/a	n/a
13	GATA3	chr2:114040064-114041988	A549	lung:	n/a	chr2:114040943-114040953
14	ELF1	chr2:114041143-114041626	A549	lung:	n/a	n/a
15	POLR2A	chr2:114041264-114041987	ECC-1	luminal epithelium:	n/a	n/a
16	NR3C1	chr2:114041179-114042004	A549	lung:	n/a	chr2:114041736-114041762
17	TCF12	chr2:114041126-114041804	A549	lung:	n/a	chr2:114041607-114041617
18	BCL3	chr2:114041201-114041826	A549	lung:	n/a	n/a
19	RAD21	chr2:114041202-114042005	ECC-1	luminal epithelium:	n/a	n/a
20	FOXM1	chr2:114040291-114042129	ECC-1	luminal epithelium:	n/a	n/a
21	FOXA2	chr2:114041241-114041784	A549	lung:	n/a	n/a
22	TEAD4	chr2:114041251-114041821	A549	lung:	n/a	n/a
23	MAX	chr2:114041275-114042057	ECC-1	luminal epithelium:	n/a	n/a
24	SIX5	chr2:114040598-114041732	A549	lung:	n/a	n/a
25	TEAD4	chr2:114041019-114041882	A549	lung:	n/a	n/a
26	STAT3	chr2:114041193-114041735	MCF10A-Er-Src	breast:	n/a	chr2:114041562-114041570
27	MYC	chr2:114040416-114041801	MCF10A-Er-Src	breast:	n/a	chr2:114040779-114040788 chr2:114040778-114040788 chr2:114040779-114040788 chr2:114040777-114040785 chr2:114040778-114040789 chr2:114040779-114040788
28	MAX	chr2:114039577-114042272	A549	lung:	n/a	chr2:114040779-114040788 chr2:114040778-114040788 chr2:114040779-114040788 chr2:114040777-114040785 chr2:114040778-114040789 chr2:114040206-114040215 chr2:114040779-114040788
29	CREB1	chr2:114041277-114041924	A549	lung:	n/a	n/a
30	TCF12	chr2:114041163-114041996	SK-N-SH	brain:	n/a	chr2:114041607-114041617
31	RXRA	chr2:114041237-114041897	SK-N-SH	brain:	n/a	n/a
32	PBX3	chr2:114041305-114041944	SK-N-SH	brain:	n/a	n/a
33	MAX	chr2:114041248-114041818	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr2:114041258-114041885	HCT-116	colon:	n/a	n/a
35	CEBPB	chr2:114040315-114041768	A549	lung:	n/a	n/a
36	NR3C1	chr2:114041322-114041831	A549	lung:	n/a	chr2:114041736-114041762
37	FOXA2	chr2:114041218-114041636	A549	lung:	n/a	n/a
38	GATA3	chr2:114041246-114041931	SK-N-SH	brain:	n/a	n/a
39	STAT3	chr2:114041179-114041904	MCF10A-Er-Src	breast:	n/a	chr2:114041562-114041570
40	POLR2A	chr2:114041322-114041848	HCT-116	colon:	n/a	n/a
41	POLR2A	chr2:114041154-114042386	U87	brain:	n/a	n/a
42	FOSL2	chr2:114041245-114041887	A549	lung:	n/a	chr2:114041379-114041389 chr2:114041381-114041392 chr2:114041380-114041388
43	POLR2A	chr2:114041355-114041888	SK-N-SH	brain:	n/a	n/a
44	CEBPB	chr2:114041258-114041910	ECC-1	luminal epithelium:	n/a	n/a
45	TAF1	chr2:114041232-114041709	ECC-1	luminal epithelium:	n/a	n/a
46	SP1	chr2:114040282-114042083	A549	lung:	n/a	chr2:114040737-114040751
47	NR3C1	chr2:114041294-114041767	A549	lung:	n/a	chr2:114041736-114041762
48	POLR2A	chr2:114041256-114041968	ECC-1	luminal epithelium:	n/a	n/a
49	EP300	chr2:114040252-114041977	A549	lung:	n/a	chr2:114041601-114041617
50	NFIC	chr2:114041174-114042021	SK-N-SH	brain:	n/a	chr2:114041688-114041704

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:114041343..114041852-chr8:123235626..123236502,2	MCF-7	breast:
2	chr2:114033208..114035776-chr2:114039656..114042402,2	K562	blood:

Variant related genes	Relation type
PAX8	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10201645	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10209795	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11123174	0.80[AMR][1000 genomes]
rs11123175	0.81[AMR][1000 genomes]
rs11679928	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11683025	0.81[AMR][1000 genomes]
rs11687706	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11688620	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11889663	0.82[AMR][1000 genomes]
rs12467534	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12989922	0.81[AMR][1000 genomes]
rs13002606	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13022812	0.80[AMR][1000 genomes]
rs13385108	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13388160	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17626434	0.83[AMR][1000 genomes]
rs17626470	0.81[AMR][1000 genomes]
rs1867763	0.80[AMR][1000 genomes]
rs34657362	0.82[AMR][1000 genomes]
rs4091938	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4848324	0.80[AMR][1000 genomes]
rs4848325	0.81[AMR][1000 genomes]
rs4848326	0.81[AMR][1000 genomes]
rs4848327	0.81[AMR][1000 genomes]
rs4848328	0.80[AMR][1000 genomes]
rs4848330	0.80[EUR][1000 genomes]
rs4849191	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4849192	0.80[AMR][1000 genomes]
rs4849194	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6753679	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6760462	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6760648	0.80[EUR][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	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
2	nsv874901	chr2:114022569-114079565	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv998204	chr2:114023917-114075446	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs7587376	PAX8	cis	Whole Blood	GTEx
rs7587376	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs7587376	PAX8	cis	Esophagus Mucosa	GTEx
rs7587376	AC016683.6	cis	Esophagus Mucosa	GTEx
rs7587376	AC016683.6	cis	Nerve Tibial	GTEx
rs7587376	PAX8	cis	lung	GTEx
rs7587376	PAX8	cis	Artery Tibial	GTEx
rs7587376	AC016683.6	cis	Whole Blood	GTEx
rs7587376	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs7587376	AC016683.6	cis	Artery Tibial	GTEx
rs7587376	AC016683.6	cis	Esophagus Muscularis	GTEx
rs7587376	PAX8	cis	Nerve Tibial	GTEx
rs7587376	AC016683.6	cis	lung	GTEx
rs7587376	AC016683.6	cis	Muscle Skeletal	GTEx
rs7587376	PAX8	cis	Esophagus Muscularis	GTEx
rs7587376	PAX8	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114036600-114043800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:114037400-114043600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:114037600-114042200	Enhancers	Pancreas	Pancrea
4	chr2:114037600-114043800	Enhancers	HMEC	breast
5	chr2:114038200-114043800	Enhancers	Fetal Intestine Large	intestine
6	chr2:114038400-114043600	Enhancers	Fetal Intestine Small	intestine
7	chr2:114038600-114043600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:114038600-114043800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:114039000-114043800	Enhancers	HSMM	muscle
10	chr2:114039200-114041800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr2:114039400-114041800	Enhancers	NH-A	brain
12	chr2:114039400-114042000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:114039400-114043000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:114039400-114043200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:114039400-114043200	Enhancers	Placenta Amnion	Placenta Amnion
16	chr2:114039600-114042200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:114039600-114042400	Enhancers	Adipose Nuclei	Adipose
18	chr2:114039600-114042600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr2:114039600-114043400	Enhancers	Osteobl	bone
20	chr2:114039600-114043600	Enhancers	HSMMtube	muscle
21	chr2:114039600-114043800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:114039800-114042200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr2:114039800-114042200	Enhancers	Stomach Mucosa	stomach
24	chr2:114039800-114043600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:114040000-114041600	Flanking Active TSS	HepG2	liver
26	chr2:114040000-114042200	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr2:114040000-114042600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:114040200-114041600	Enhancers	Colonic Mucosa	Colon
29	chr2:114040200-114041800	Enhancers	Right Ventricle	heart
30	chr2:114040200-114042600	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr2:114040400-114042000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:114040400-114042000	Enhancers	Placenta	Placenta
33	chr2:114040400-114042200	Enhancers	Fetal Heart	heart
34	chr2:114040400-114042400	Enhancers	Fetal Muscle Leg	muscle
35	chr2:114040400-114042400	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr2:114040400-114042400	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr2:114040400-114042800	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr2:114040600-114041600	Enhancers	Right Atrium	heart
39	chr2:114040600-114041800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:114040600-114041800	Weak transcription	Aorta	Aorta
41	chr2:114040600-114041800	Weak transcription	Fetal Kidney	kidney
42	chr2:114040600-114042200	Enhancers	Left Ventricle	heart
43	chr2:114040600-114043600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:114040600-114043600	Enhancers	Colon Smooth Muscle	Colon
45	chr2:114040600-114043600	Enhancers	NHDF-Ad	bronchial
46	chr2:114040600-114047000	Enhancers	Liver	Liver
47	chr2:114040600-114047800	Weak transcription	Gastric	stomach
48	chr2:114040800-114042200	Enhancers	Fetal Muscle Trunk	muscle
49	chr2:114040800-114042400	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr2:114040800-114042400	Enhancers	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links