Variant report

Variant	rs745912
Chromosome Location	chr2:113998332-113998333
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	MAX	chr2:113998216-113999609	SK-N-SH	brain:	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
2	SIX5	chr2:113997662-113999126	A549	lung:	n/a	n/a
3	SMARCC1	chr2:113997660-113999427	Hela-S3	cervix:	n/a	chr2:113999386-113999395
4	POLR2A	chr2:113998242-113999021	HCT-116	colon:	n/a	n/a
5	GATA3	chr2:113998285-113999134	A549	lung:	n/a	n/a
6	POLR2A	chr2:113997003-114000128	IMR90	lung:	n/a	n/a
7	FOS	chr2:113997803-113999533	MCF10A-Er-Src	breast:	n/a	chr2:113999384-113999396 chr2:113998584-113998595 chr2:113999387-113999398 chr2:113999385-113999395 chr2:113999385-113999395 chr2:113999386-113999394
8	FOSL2	chr2:113997326-113999659	A549	lung:	n/a	chr2:113999384-113999396 chr2:113999387-113999398 chr2:113999385-113999395 chr2:113999385-113999395 chr2:113998585-113998596 chr2:113999386-113999394
9	USF1	chr2:113998126-113999212	A549	lung:	n/a	n/a
10	E2F6	chr2:113998194-113999726	A549	lung:	n/a	n/a
11	POLR2A	chr2:113996944-114000866	K562	blood:	n/a	n/a
12	JUND	chr2:113998307-113998983	HepG2	liver:	n/a	chr2:113998584-113998595
13	SP1	chr2:113997527-113999233	A549	lung:	n/a	n/a
14	USF1	chr2:113998286-113999005	A549	lung:	n/a	n/a
15	GABPA	chr2:113998062-113999089	A549	lung:	n/a	n/a
16	ZNF263	chr2:113997802-113998805	HEK293-T-REx	kidney:	n/a	n/a
17	NFIC	chr2:113998310-113998943	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr2:113997475-113999254	GM12878	blood:	n/a	n/a
19	MAX	chr2:113997698-113999070	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr2:113997827-113999157	MCF10A-Er-Src	breast:	n/a	n/a
21	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
22	FOSL1	chr2:113997636-113999713	HCT-116	colon:	n/a	chr2:113999384-113999396 chr2:113999387-113999398 chr2:113999385-113999395 chr2:113999385-113999395 chr2:113999386-113999394
23	EP300	chr2:113998276-113999029	Hela-S3	cervix:	n/a	n/a
24	TCF12	chr2:113998298-113999050	A549	lung:	n/a	n/a
25	TCF12	chr2:113997628-113999335	SK-N-SH	brain:	n/a	n/a
26	STAT3	chr2:113997845-113999093	MCF10A-Er-Src	breast:	n/a	n/a
27	SIN3AK20	chr2:113998245-113999178	MCF-7	breast:	n/a	n/a
28	POLR2A	chr2:113998319-113999234	GM12892	blood:	n/a	n/a
29	NR3C1	chr2:113998209-113999105	A549	lung:	n/a	n/a
30	ATF3	chr2:113998255-113999144	A549	lung:	n/a	n/a
31	CEBPB	chr2:113998274-113999241	A549	lung:	n/a	chr2:113998825-113998836
32	MXI1	chr2:113997343-113999336	IMR90	lung:	n/a	n/a
33	FOSL2	chr2:113998320-113998938	MCF-7	breast:	n/a	chr2:113998585-113998596
34	POLR2A	chr2:113998294-113999102	K562	blood:	n/a	n/a
35	MYC	chr2:113997694-113999664	MCF10A-Er-Src	breast:	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
36	CEBPB	chr2:113997382-113999188	IMR90	lung:	n/a	chr2:113998825-113998836
37	JUND	chr2:113997140-113999306	SK-N-SH	brain:	n/a	chr2:113998584-113998595
38	GATA3	chr2:113997609-113999117	SK-N-SH	brain:	n/a	n/a
39	CEBPB	chr2:113997572-113999797	HCT-116	colon:	n/a	chr2:113998825-113998836
40	YY1	chr2:113998330-113998945	A549	lung:	n/a	n/a
41	SIN3AK20	chr2:113997752-113999111	A549	lung:	n/a	n/a
42	FOSL2	chr2:113998265-113998949	SK-N-SH	brain:	n/a	chr2:113998585-113998596
43	ATF3	chr2:113998239-113999189	A549	lung:	n/a	n/a
44	MAZ	chr2:113998318-113998874	HepG2	liver:	n/a	n/a
45	RAD21	chr2:113997940-113999037	A549	lung:	n/a	n/a
46	NFIC	chr2:113997502-113999532	SK-N-SH	brain:	n/a	n/a
47	TCF12	chr2:113997522-113999698	SK-N-SH	brain:	n/a	n/a
48	FOSL2	chr2:113998258-113998958	HepG2	liver:	n/a	chr2:113998585-113998596
49	POLR2A	chr2:113997465-113999660	U87	brain:	n/a	n/a
50	CTCF	chr2:113998220-113998370	AG04450	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:113952804..113954880-chr2:113996400..113999228,2	MCF-7	breast:
2	chr2:113950220..113951864-chr2:113997428..113999954,2	K562	blood:
3	chr17:79828317..79829241-chr2:113997773..113998684,2	HCT-116	colon:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSD4-1	chr2:113996666-113998402	ENSG00000189223
2	lnc-PSD4-1	chr2:113998307-113998678	ENSG00000258395
3	lnc-PSD4-1	chr2:113996666-113998419	NONHSAT073761

Variant related genes	Relation type
PAX8	TF binding region
ENSG00000125637	Chromatin interaction
ENSG00000141522	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1021409	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12467324	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12471722	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12998725	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2003986	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738913	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4848320	0.81[AMR][1000 genomes]
rs4849186	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs745912	AC016683.6	cis	Whole Blood	GTEx
rs745912	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs745912	PAX8	cis	lung	GTEx
rs745912	AC016683.6	cis	lung	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

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	chr2:113994800-113998600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:113994800-114006600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr2:113995000-113998800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:113995000-114006800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:113995200-114000000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr2:113995200-114007000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr2:113995400-113999000	Enhancers	Fetal Muscle Leg	muscle
13	chr2:113995600-114000200	Weak transcription	Dnd41	blood
14	chr2:113995600-114008600	Weak transcription	GM12878-XiMat	blood
15	chr2:113995800-113999000	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr2:113996200-113998800	Genic enhancers	Fetal Kidney	kidney
17	chr2:113996600-114000200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:113996800-113998400	Enhancers	HepG2	liver
19	chr2:113996800-113998600	Enhancers	Fetal Muscle Trunk	muscle
20	chr2:113996800-113999000	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr2:113997000-113998800	Enhancers	Liver	Liver
22	chr2:113997000-113999000	Enhancers	Primary hematopoietic stem cells	blood
23	chr2:113997000-113999000	Enhancers	Fetal Lung	lung
24	chr2:113997000-113999200	Enhancers	Brain Anterior Caudate	brain
25	chr2:113997000-113999200	Enhancers	Brain Cingulate Gyrus	brain
26	chr2:113997000-113999200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:113997000-113999200	Enhancers	Placenta	Placenta
28	chr2:113997000-113999200	Enhancers	Gastric	stomach
29	chr2:113997000-113999200	Enhancers	Right Atrium	heart
30	chr2:113997000-113999200	Genic enhancers	K562	blood
31	chr2:113997000-113999400	Enhancers	Colonic Mucosa	Colon
32	chr2:113997000-113999400	Enhancers	Spleen	Spleen
33	chr2:113997000-113999600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:113997000-113999600	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr2:113997000-114000000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:113997000-114000000	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr2:113997000-114000000	Enhancers	Placenta Amnion	Placenta Amnion
38	chr2:113997000-114000600	Enhancers	Esophagus	oesophagus
39	chr2:113997200-113999200	Enhancers	Brain Germinal Matrix	brain
40	chr2:113997200-113999200	Flanking Active TSS	Hela-S3	cervix
41	chr2:113997200-113999600	Enhancers	Stomach Mucosa	stomach
42	chr2:113997400-113998400	Flanking Active TSS	A549	lung
43	chr2:113997400-113998600	Flanking Active TSS	NHEK	skin
44	chr2:113997400-113998800	Enhancers	Rectal Smooth Muscle	rectum
45	chr2:113997400-113999000	Enhancers	Colon Smooth Muscle	Colon
46	chr2:113997400-113999200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:113997400-113999200	Enhancers	Duodenum Mucosa	Duodenum
48	chr2:113997400-113999200	Enhancers	Pancreas	Pancrea
49	chr2:113997400-113999200	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr2:113997400-113999400	Enhancers	HUVEC	blood vessel

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