Variant report

Variant	rs7589901
Chromosome Location	chr2:113993344-113993345
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:97)
CpG islands
(count:122)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:97 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr2:113992825-113993468	NB4	blood:	n/a	n/a
2	MYC	chr2:113993134-113993396	MCF-7	breast:	n/a	n/a
3	MYC	chr2:113992469-113993469	K562	blood:	n/a	n/a
4	POLR2A	chr2:113992818-113993349	PBDE	blood:	n/a	n/a
5	GABPA	chr2:113992739-113993568	MCF-7	breast:	n/a	chr2:113993256-113993265 chr2:113993249-113993258
6	MAX	chr2:113993005-113993409	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:113992805-113993499	GM18505	blood:	n/a	n/a
8	MAX	chr2:113992430-113993533	HCT-116	colon:	n/a	n/a
9	E2F6	chr2:113992866-113993435	K562	blood:	n/a	chr2:113993249-113993258
10	TEAD4	chr2:113992919-113993434	K562	blood:	n/a	n/a
11	TAF1	chr2:113992908-113993453	K562	blood:	n/a	n/a
12	MYC	chr2:113993107-113993346	MCF-7	breast:	n/a	n/a
13	POLR2A	chr2:113992830-113993455	PFSK-1	brain:	n/a	n/a
14	ETS1	chr2:113993180-113993389	K562	blood:	n/a	chr2:113993247-113993258
15	MAX	chr2:113992607-113993492	K562	blood:	n/a	n/a
16	TAF1	chr2:113992885-113993488	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:113992717-113993443	HCT-116	colon:	n/a	n/a
18	UBTF	chr2:113992948-113993428	K562	blood:	n/a	n/a
19	ELF1	chr2:113992815-113993485	MCF-7	breast:	n/a	n/a
20	ELF1	chr2:113992865-113993502	K562	blood:	n/a	n/a
21	POLR2A	chr2:113992768-113993377	HCT-116	colon:	n/a	n/a
22	MAX	chr2:113992844-113993446	K562	blood:	n/a	n/a
23	YY1	chr2:113992652-113993417	K562	blood:	n/a	chr2:113993199-113993207
24	POLR2A	chr2:113992566-113993492	ECC-1	luminal epithelium:	n/a	n/a
25	MYC	chr2:113992518-113993471	K562	blood:	n/a	n/a
26	POLR2A	chr2:113992646-113993615	K562	blood:	n/a	n/a
27	POLR2A	chr2:113992787-113993366	K562	blood:	n/a	n/a
28	POLR2A	chr2:113992776-113993364	K562	blood:	n/a	n/a
29	TAF1	chr2:113992920-113993348	PFSK-1	brain:	n/a	n/a
30	HMGN3	chr2:113992791-113993375	K562	blood:	n/a	n/a
31	YY1	chr2:113992752-113993454	GM12892	blood:	n/a	chr2:113993199-113993207
32	CCNT2	chr2:113992848-113993447	K562	blood:	n/a	n/a
33	POLR2A	chr2:113992474-113993420	HCT-116	colon:	n/a	n/a
34	ZBTB7A	chr2:113993265-113993477	K562	blood:	n/a	n/a
35	HEY1	chr2:113992739-113993449	K562	blood:	n/a	chr2:113993246-113993261 chr2:113993251-113993266
36	POLR2A	chr2:113992771-113993517	GM18526	blood:	n/a	n/a
37	POLR2A	chr2:113992815-113993505	K562	blood:	n/a	n/a
38	MAX	chr2:113992829-113993443	K562	blood:	n/a	n/a
39	ELF1	chr2:113993125-113993490	K562	blood:	n/a	n/a
40	GABPA	chr2:113992801-113993385	K562	blood:	n/a	chr2:113993256-113993265 chr2:113993249-113993258
41	POLR2A	chr2:113992779-113993410	K562	blood:	n/a	n/a
42	POLR2A	chr2:113992836-113993367	GM12878	blood:	n/a	n/a
43	E2F6	chr2:113992478-113993456	K562	blood:	n/a	chr2:113992603-113992620 chr2:113993249-113993258 chr2:113992626-113992640
44	POLR2A	chr2:113992778-113993504	MCF-7	breast:	n/a	n/a
45	POLR2A	chr2:113992866-113993417	K562	blood:	n/a	n/a
46	POLR2A	chr2:113992720-113993432	GM12878	blood:	n/a	n/a
47	CBX3	chr2:113992877-113993435	K562	blood:	n/a	n/a
48	POLR2A	chr2:113992805-113993415	GM12892	blood:	n/a	n/a
49	POLR2A	chr2:113992796-113993475	ProgFib	skin:	n/a	n/a
50	POLR2A	chr2:113992769-113994217	GM12892	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:113993304-113993354	SKMC	muscle:	n/a
2	chr2:113993304-113993354	SAEC	small airway:	n/a
3	chr2:113993304-113993354	Hela-S3	cervix:	n/a
4	chr2:113993313-113993363	U87	brain:	n/a
5	chr2:113993304-113993354	K562	blood:	n/a
6	chr2:113993304-113993354	T-47D	breast:	n/a
7	chr2:113993304-113993354	A549	lung:	n/a
8	chr2:113993304-113993354	HEEpiC	esophagus:	n/a
9	chr2:113993313-113993363	SKMC	muscle:	n/a
10	chr2:113993313-113993363	PrEC	prostate:	n/a
11	chr2:113993313-113993363	NB4	blood:	n/a
12	chr2:113993313-113993363	ProgFib	skin:	n/a
13	chr2:113993313-113993363	AG04450	lung:	fetal
14	chr2:113993304-113993354	GM12878	blood:	n/a
15	chr2:113993304-113993354	HCPEpiC	choroid plexus:	n/a
16	chr2:113993304-113993354	CMK	blood:	n/a
17	chr2:113993304-113993354	GM06990	blood:	n/a
18	chr2:113993313-113993363	SK-N-SH	brain:	n/a
19	chr2:113993304-113993354	Hepatocyte	liver:	n/a
20	chr2:113993313-113993363	SK-N-MC	brain:	n/a
21	chr2:113993304-113993354	NT2-D1	testis:	n/a
22	chr2:113993313-113993363	AG10803	skin:	n/a
23	chr2:113993304-113993354	AG04450	lung:	fetal
24	chr2:113993313-113993363	BJ	skin:	n/a
25	chr2:113993313-113993363	A549	lung:	n/a
26	chr2:113993304-113993354	Jurkat	blood:	n/a
27	chr2:113993304-113993354	IMR90	lung:	fetal
28	chr2:113993304-113993354	AG09309	skin:	n/a
29	chr2:113993313-113993363	NHBE	bronchial:	n/a
30	chr2:113993313-113993363	GM12891	blood:	n/a
31	chr2:113993304-113993354	HPAEpiC	pulmonary alveolar:	n/a
32	chr2:113993313-113993363	HEK293	kidney:	embryo
33	chr2:113993304-113993354	MCF-7	breast:	n/a
34	chr2:113993313-113993363	HepG2	liver:	n/a
35	chr2:113993304-113993354	HCM	heart:	n/a
36	chr2:113993304-113993354	SK-N-SH_RA	brain:	n/a
37	chr2:113993313-113993363	HRPEpiC	eye:	n/a
38	chr2:113993313-113993363	HRE	kidney:	n/a
39	chr2:113993304-113993354	ovcar-3	ovarian:	n/a
40	chr2:113993304-113993354	HIPEpiC	eye:	n/a
41	chr2:113993304-113993354	HCT-116	colon:	n/a
42	chr2:113993313-113993363	AoSMC	blood vessel:	n/a
43	chr2:113993313-113993363	Jurkat	blood:	n/a
44	chr2:113993313-113993363	HMEC	breast:	n/a
45	chr2:113993304-113993354	RPTEC	kidney:	n/a
46	chr2:113993304-113993354	GM19239	blood:	n/a
47	chr2:113993304-113993354	HMEC	breast:	n/a
48	chr2:113993304-113993354	BE2_C	brain:	n/a
49	chr2:113993313-113993363	GM12892	blood:	n/a
50	chr2:113993313-113993363	HEEpiC	esophagus:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr2:113992705..113993646-chr6:26123786..26124566,2	HCT-116	colon:
2	chr2:113968914..113973967-chr2:113991743..113995400,6	MCF-7	breast:
3	chr2:113968482..113971643-chr2:113991034..113994286,5	MCF-7	breast:
4	chr2:113973621..113980487-chr2:113991287..113996231,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000258395	TF binding region
PAX8-AS1	TF binding region
PAX8	TF binding region
PAX8	CpG island
PAX8-AS1	CpG island
ENSG00000258395	CpG island
ENSG00000180573	Chromatin interaction
ENSG00000189223	Chromatin interaction
ENSG00000125618	Chromatin interaction
ENSG00000180596	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 26 )

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

rs_ID	r²[population]
rs10175462	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10206269	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1110839	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11123170	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11123172	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12619508	0.82[ASN][1000 genomes]
rs12620738	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2019137	0.83[ASN][1000 genomes]
rs2863243	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3748916	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3811059	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs4849176	0.89[ASN][1000 genomes]
rs4849177	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4849179	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4849181	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849183	0.93[ASN][1000 genomes]
rs6707386	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6751201	0.82[JPT][hapmap]
rs6755040	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6755639	0.89[ASN][1000 genomes]
rs731834	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs7421852	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7563094	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7572615	0.81[AFR][1000 genomes]
rs7576384	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7578633	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs874898	0.88[JPT][hapmap]
rs895412	0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs902695	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs902696	0.85[CHB][hapmap];0.94[JPT][hapmap]

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:26)

SNP	Gene	Cis/trans	Tissue	Source
rs7589901	PAX8	cis	Nerve Tibial	GTEx
rs7589901	PAX8	cis	Adipose Subcutaneous	GTEx
rs7589901	PAX8	cis	Esophagus Muscularis	GTEx
rs7589901	AC016683.6	cis	Esophagus Muscularis	GTEx
rs7589901	PAX8	cis	Stomach	GTEx
rs7589901	AC016683.6	cis	Esophagus Mucosa	GTEx
rs7589901	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs7589901	PAX8	cis	Artery Aorta	GTEx
rs7589901	AC016683.6	cis	Artery Aorta	GTEx
rs7589901	PAX8	cis	multi-tissue	Pritchard
rs7589901	AC016683.6	cis	Stomach	GTEx
rs7589901	PAX8	cis	Artery Tibial	GTEx
rs7589901	PAX8	cis	lung	GTEx
rs7589901	PAX8	Cis_1M	lymphoblastoid	RTeQTL
rs7589901	RP11-65I12.1	cis	Esophagus Mucosa	GTEx
rs7589901	PAX8	cis	Esophagus Mucosa	GTEx
rs7589901	PAX8	cis	Skin Sun Exposed Lower leg	GTEx
rs7589901	AC016683.6	cis	Muscle Skeletal	GTEx
rs7589901	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs7589901	AC016683.6	cis	Artery Tibial	GTEx
rs7589901	AC016683.6	cis	Heart Left Ventricle	GTEx
rs7589901	AC016683.6	cis	Skin Sun Exposed Lower leg	GTEx
rs7589901	AC016683.6	cis	Nerve Tibial	GTEx
rs7589901	AC016683.6	cis	Whole Blood	GTEx
rs7589901	AC016683.6	cis	lung	GTEx
rs7589901	PAX8	cis	Whole Blood	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113984000-113998000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:113987000-113997000	Weak transcription	Hela-S3	cervix
3	chr2:113991800-113997000	Weak transcription	Spleen	Spleen
4	chr2:113992000-113994800	Weak transcription	HepG2	liver
5	chr2:113992000-113997000	Weak transcription	Esophagus	oesophagus
6	chr2:113992000-113997000	Weak transcription	Fetal Heart	heart
7	chr2:113992000-113997000	Weak transcription	Right Atrium	heart
8	chr2:113992000-113997400	Weak transcription	Left Ventricle	heart
9	chr2:113992000-113997400	Weak transcription	Right Ventricle	heart
10	chr2:113992400-113993400	Active TSS	GM12878-XiMat	blood
11	chr2:113992600-113993400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:113992600-113993400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr2:113992600-113993400	Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr2:113992600-113993400	Active TSS	Liver	Liver
15	chr2:113992600-113993400	ZNF genes & repeats	Fetal Thymus	thymus
16	chr2:113992600-113993400	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr2:113992600-113993400	Active TSS	Monocytes-CD14+_RO01746	blood
18	chr2:113992600-113993600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr2:113992600-113993600	Active TSS	Fetal Intestine Small	intestine
20	chr2:113992600-113993600	Active TSS	Fetal Stomach	stomach
21	chr2:113992600-113993600	Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr2:113992600-113993800	Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr2:113992600-113994000	Active TSS	Fetal Brain Female	brain
24	chr2:113992600-113994000	Active TSS	Ovary	ovary
25	chr2:113992600-113994200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr2:113992600-113994200	Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr2:113992600-113994200	Active TSS	Adipose Nuclei	Adipose
28	chr2:113992600-113994200	Active TSS	Placenta Amnion	Placenta Amnion
29	chr2:113992600-113994200	Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr2:113992600-113994400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:113992600-113994400	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr2:113992600-113994400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr2:113992600-113994400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:113992600-113994400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:113992600-113994400	Active TSS	Colonic Mucosa	Colon
36	chr2:113992600-113994400	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr2:113992600-113994400	Active TSS	HSMMtube	muscle
38	chr2:113992600-113994600	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr2:113992600-113994600	Active TSS	Brain Hippocampus Middle	brain
40	chr2:113992600-113994600	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr2:113992600-113994600	Active TSS	Fetal Intestine Large	intestine
42	chr2:113992600-113994800	Active TSS	Duodenum Mucosa	Duodenum
43	chr2:113992600-113995000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:113992600-113995000	Active TSS	HSMM	muscle
45	chr2:113992600-113995200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:113992600-113995200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:113992600-113995200	Active TSS	Osteobl	bone
48	chr2:113992600-113995400	Active TSS	Muscle Satellite Cultured Cells	--
49	chr2:113992800-113993400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:113992800-113993400	Active TSS	Primary hematopoietic stem cells	blood

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