Variant report

Variant	rs13429413
Chromosome Location	chr2:114006834-114006835
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	CTCF	chr2:114006714-114007077	K562	blood:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
2	CTCF	chr2:114006733-114007065	SK-N-SH_RA	brain:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
3	CTCF	chr2:114006764-114007062	GM19239	blood:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
4	STAT3	chr2:114006806-114007019	MCF10A-Er-Src	breast:	n/a	chr2:114006991-114007002
5	FOXM1	chr2:114006677-114007184	GM12878	blood:	n/a	n/a
6	RFX5	chr2:114006771-114007124	Hela-S3	cervix:	n/a	n/a
7	NFIC	chr2:114006641-114007062	HepG2	liver:	n/a	n/a
8	MXI1	chr2:114006729-114007067	HepG2	liver:	n/a	n/a
9	MAZ	chr2:114006804-114007047	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr2:114006779-114007074	HUVEC	blood vessel:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
11	CTCF	chr2:114006820-114006970	WERI-Rb-1	eye:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
12	CTCF	chr2:114006776-114007057	MCF-7	breast:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
13	RAD21	chr2:114006714-114007373	IMR90	lung:	n/a	chr2:114006923-114006942
14	JUND	chr2:114006762-114007104	K562	blood:	n/a	n/a
15	MBD4	chr2:114006680-114007156	HepG2	liver:	n/a	n/a
16	CTCF	chr2:114006767-114007079	K562	blood:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
17	ZNF143	chr2:114006742-114007085	H1-hESC	embryonic stem cell:	n/a	n/a
18	JUND	chr2:114006820-114007111	H1-hESC	embryonic stem cell:	n/a	n/a
19	YY1	chr2:114006759-114007047	GM12891	blood:	n/a	n/a
20	ZNF263	chr2:114006667-114007134	HEK293-T-REx	kidney:	n/a	n/a
21	CTCF	chr2:114006816-114007004	A549	lung:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
22	CTCF	chr2:114006820-114006970	HMEC	breast:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
23	SMC3	chr2:114006711-114007206	GM12878	blood:	n/a	chr2:114006924-114006938
24	CTCF	chr2:114006726-114007047	A549	lung:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
25	CTCF	chr2:114006820-114006970	SAEC	small airway:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
26	MYC	chr2:114006789-114007036	MCF10A-Er-Src	breast:	n/a	n/a
27	SMC3	chr2:114006735-114007127	K562	blood:	n/a	chr2:114006924-114006938
28	YY1	chr2:114006762-114007008	HCT-116	colon:	n/a	n/a
29	YY1	chr2:114006691-114007094	GM12878	blood:	n/a	n/a
30	CTCF	chr2:114006482-114007371	HCT-116	colon:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
31	SMC3	chr2:114006681-114007243	Hela-S3	cervix:	n/a	chr2:114006924-114006938
32	YY1	chr2:114006768-114007059	SK-N-SH_RA	brain:	n/a	n/a
33	CTCF	chr2:114006713-114007165	K562	blood:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
34	CTCF	chr2:114006799-114007053	HepG2	liver:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
35	YY1	chr2:114006766-114007047	HepG2	liver:	n/a	n/a
36	CTCF	chr2:114006732-114007070	H1-hESC	embryonic stem cell:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
37	HCFC1	chr2:114006760-114007015	K562	blood:	n/a	n/a
38	CTCF	chr2:114006803-114007049	GM10248	blood:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
39	RAD21	chr2:114006706-114007184	SK-N-SH_RA	brain:	n/a	chr2:114006923-114006942
40	MAX	chr2:114006516-114007278	A549	lung:	n/a	n/a
41	RAD21	chr2:114006678-114007215	MCF-7	breast:	n/a	chr2:114006923-114006942
42	CTCF	chr2:114006780-114006930	HRE	kidney:	n/a	n/a
43	CTCF	chr2:114006645-114007108	T-47D	breast:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
44	BRCA1	chr2:114006810-114007085	Hela-S3	cervix:	n/a	n/a
45	RCOR1	chr2:114006769-114007076	HepG2	liver:	n/a	n/a
46	ZNF384	chr2:114006789-114007164	K562	blood:	n/a	n/a
47	CTCF	chr2:114006744-114007080	NHEK	skin:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
48	CTCF	chr2:114006721-114007087	GM12892	blood:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
49	CTCF	chr2:114006820-114006970	HFF-Myc	foreskin:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940
50	CTCF	chr2:114006686-114007101	K562	blood:	n/a	chr2:114006923-114006939 chr2:114006924-114006945 chr2:114006927-114006937 chr2:114006922-114006940

No.	Distal block	Cell Line	Cell type
1	chr2:114000063..114003907-chr2:114004909..114007665,4	MCF-7	breast:
2	chr2:114006181..114007719-chr2:114012379..114015076,2	K562	blood:
3	chr2:114006796..114007421-chr2:114127816..114128725,5	K562	blood:
4	chr2:114006461..114007910-chr2:114147631..114148371,4	K562	blood:
5	chr2:114006433..114007490-chr2:114127813..114128753,6	MCF-7	breast:
6	chr2:114006491..114007402-chr2:114127850..114128740,6	MCF-7	breast:

Variant related genes	Relation type
PAX8-AS1	TF binding region
ENSG00000189223	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11123173	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12990456	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1491585	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1491586	0.83[ASN][1000 genomes]
rs2863244	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35129549	0.83[ASN][1000 genomes]
rs4142815	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4849187	0.87[ASN][1000 genomes]
rs6542127	0.81[EUR][1000 genomes]
rs6726151	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6734610	0.88[EUR][1000 genomes];0.86[ASN][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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs13429413	RP11-65I12.1	cis	Thyroid	GTEx
rs13429413	PAX8	cis	Esophagus Muscularis	GTEx
rs13429413	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs13429413	AC016683.6	cis	lung	GTEx
rs13429413	AC016683.6	cis	Esophagus Mucosa	GTEx
rs13429413	AC016683.6	cis	Esophagus Muscularis	GTEx
rs13429413	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs13429413	AC016683.6	cis	Artery Tibial	GTEx
rs13429413	PAX8	cis	Adipose Subcutaneous	GTEx
rs13429413	PAX8	cis	Esophagus Mucosa	GTEx
rs13429413	AC016683.6	cis	Whole Blood	GTEx
rs13429413	AC016683.6	cis	Muscle Skeletal	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113995200-114007000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr2:113995600-114008600	Weak transcription	GM12878-XiMat	blood
3	chr2:113998200-114020600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr2:113999000-114014800	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:113999200-114007000	Weak transcription	Right Atrium	heart
6	chr2:113999200-114009400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr2:113999200-114013200	Weak transcription	Placenta	Placenta
8	chr2:113999400-114009400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:113999600-114007000	Weak transcription	HSMMtube	muscle
10	chr2:113999600-114013200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:113999600-114016400	Weak transcription	Fetal Stomach	stomach
12	chr2:113999600-114028400	Weak transcription	Ovary	ovary
13	chr2:114000000-114007000	Weak transcription	HSMM	muscle
14	chr2:114000200-114009200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:114000200-114012000	Weak transcription	NHDF-Ad	bronchial
16	chr2:114000600-114011000	Weak transcription	Esophagus	oesophagus
17	chr2:114002400-114015400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:114003600-114007000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:114003600-114008400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:114004000-114007000	Weak transcription	Primary T cells from cord blood	blood
21	chr2:114004200-114007000	Weak transcription	HepG2	liver
22	chr2:114004200-114008800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:114004800-114010600	Weak transcription	Fetal Kidney	kidney
24	chr2:114005600-114008600	Weak transcription	Lung	lung
25	chr2:114006000-114007000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:114006000-114008000	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr2:114006000-114008800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:114006400-114007000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:114006400-114009000	Enhancers	HMEC	breast
30	chr2:114006600-114007000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:114006600-114007000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:114006600-114007000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
33	chr2:114006600-114007000	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr2:114006600-114007200	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr2:114006600-114007200	Enhancers	Primary B cells from peripheral blood	blood
36	chr2:114006600-114007200	Enhancers	Muscle Satellite Cultured Cells	--
37	chr2:114006600-114007200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:114006600-114007200	Enhancers	Brain Substantia Nigra	brain
39	chr2:114006600-114007200	Enhancers	Fetal Intestine Large	intestine
40	chr2:114006600-114007200	Enhancers	Fetal Intestine Small	intestine
41	chr2:114006600-114007200	Enhancers	Fetal Thymus	thymus
42	chr2:114006600-114007200	Enhancers	Thymus	Thymus
43	chr2:114006600-114007400	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr2:114006600-114007400	Enhancers	Primary T cells fromperipheralblood	blood
45	chr2:114006600-114007400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:114006600-114007400	Enhancers	Adipose Nuclei	Adipose
47	chr2:114006600-114007400	Enhancers	Liver	Liver
48	chr2:114006600-114007400	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr2:114006600-114007400	Enhancers	NHEK	skin
50	chr2:114006600-114007600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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