Variant report

Variant	rs1015753
Chromosome Location	chr2:113968803-113968804
allele	A/C
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	ATF3	chr2:113968799-113969566	A549	lung:	n/a	n/a
2	MAFK	chr2:113968745-113969538	Hela-S3	cervix:	n/a	chr2:113969427-113969437 chr2:113969426-113969441 chr2:113969423-113969439 chr2:113968931-113968941 chr2:113969421-113969441 chr2:113969424-113969438
3	EP300	chr2:113968644-113970016	A549	lung:	n/a	chr2:113969881-113969891 chr2:113969547-113969561 chr2:113969533-113969547 chr2:113969553-113969567
4	SRF	chr2:113968529-113969549	HCT-116	colon:	n/a	chr2:113969013-113969024 chr2:113969014-113969028 chr2:113969010-113969024 chr2:113969014-113969023 chr2:113969012-113969025 chr2:113969013-113969027 chr2:113969010-113969028 chr2:113969012-113969025 chr2:113969011-113969026 chr2:113969008-113969026 chr2:113969013-113969030 chr2:113969010-113969027
5	MAX	chr2:113968563-113969518	A549	lung:	n/a	chr2:113969423-113969433
6	REST	chr2:113968586-113969333	A549	lung:	n/a	n/a
7	FOSL2	chr2:113968687-113969600	A549	lung:	n/a	n/a
8	MAX	chr2:113968740-113969255	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr2:113968736-113972136	ECC-1	luminal epithelium:	n/a	n/a
10	SRF	chr2:113968749-113969360	MCF-7	breast:	n/a	chr2:113969013-113969024 chr2:113969014-113969028 chr2:113969010-113969024 chr2:113969014-113969023 chr2:113969012-113969025 chr2:113969013-113969027 chr2:113969010-113969028 chr2:113969012-113969025 chr2:113969011-113969026 chr2:113969008-113969026 chr2:113969013-113969030 chr2:113969010-113969027
11	SRF	chr2:113968605-113969526	HCT-116	colon:	n/a	chr2:113969013-113969024 chr2:113969014-113969028 chr2:113969010-113969024 chr2:113969014-113969023 chr2:113969012-113969025 chr2:113969013-113969027 chr2:113969010-113969028 chr2:113969012-113969025 chr2:113969011-113969026 chr2:113969008-113969026 chr2:113969013-113969030 chr2:113969010-113969027
12	TEAD4	chr2:113968704-113969293	ECC-1	luminal epithelium:	n/a	n/a
13	GATA3	chr2:113968598-113970173	A549	lung:	n/a	chr2:113969528-113969539
14	GTF2F1	chr2:113968755-113969367	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr2:113968512-113970098	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr2:113968757-113969330	Hela-S3	cervix:	n/a	n/a
17	SP1	chr2:113968665-113970223	A549	lung:	n/a	chr2:113968984-113968994 chr2:113968984-113968994
18	JUND	chr2:113968798-113969315	A549	lung:	n/a	n/a
19	TBP	chr2:113968695-113969245	Hela-S3	cervix:	n/a	n/a
20	MAX	chr2:113967936-113970355	A549	lung:	n/a	chr2:113969423-113969433
21	TEAD4	chr2:113968616-113969352	ECC-1	luminal epithelium:	n/a	n/a
22	EP300	chr2:113968587-113969443	ECC-1	luminal epithelium:	n/a	n/a
23	TCF12	chr2:113968462-113970213	A549	lung:	n/a	chr2:113969393-113969401
24	EP300	chr2:113968642-113969471	A549	lung:	n/a	n/a
25	E2F6	chr2:113968667-113970156	A549	lung:	n/a	chr2:113969630-113969637 chr2:113969420-113969427 chr2:113969419-113969431 chr2:113969420-113969427 chr2:113969630-113969637 chr2:113969630-113969637 chr2:113969420-113969427
26	RCOR1	chr2:113968758-113969145	Hela-S3	cervix:	n/a	n/a
27	TAF1	chr2:113968761-113969333	A549	lung:	n/a	n/a
28	POLR2A	chr2:113968618-113969345	MCF10A-Er-Src	breast:	n/a	n/a
29	SRF	chr2:113968732-113969417	ECC-1	luminal epithelium:	n/a	chr2:113969013-113969024 chr2:113969014-113969028 chr2:113969010-113969024 chr2:113969014-113969023 chr2:113969012-113969025 chr2:113969013-113969027 chr2:113969010-113969028 chr2:113969012-113969025 chr2:113969011-113969026 chr2:113969008-113969026 chr2:113969013-113969030 chr2:113969010-113969027
30	SP1	chr2:113968600-113969578	A549	lung:	n/a	chr2:113968984-113968994 chr2:113968984-113968994
31	POLR2A	chr2:113968647-113972171	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr2:113968434-113969401	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:113968482..113971643-chr2:113991034..113994286,5	MCF-7	breast:
2	chr2:113031655..113033342-chr2:113967822..113970476,2	K562	blood:
3	chr2:113967701..113970551-chr2:113977130..113979448,2	K562	blood:

Variant related genes	Relation type
PAX8-AS1	TF binding region
ENSG00000189223	Chromatin interaction
ENSG00000125618	Chromatin interaction
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1015755	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1049137	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1077855	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12472361	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2166421	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2289897	0.88[AMR][1000 genomes]
rs28522253	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2863242	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28679654	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35222158	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35606997	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3738913	0.85[ASN][1000 genomes]
rs4849178	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4849180	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4849182	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6736334	0.92[AMR][1000 genomes];0.87[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	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv582712	chr2:113932431-113985170	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1015753	AC016683.6	cis	Muscle Skeletal	GTEx
rs1015753	PAX8	cis	Whole Blood	GTEx
rs1015753	AC016683.6	cis	Artery Tibial	GTEx
rs1015753	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs1015753	AC016683.6	cis	Whole Blood	GTEx
rs1015753	AC016683.6	cis	lung	GTEx
rs1015753	PAX8	cis	lung	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113957200-113969000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr2:113957200-113969000	Weak transcription	Right Atrium	heart
3	chr2:113957400-113969000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:113957400-113982600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:113958000-113975200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:113960600-113975200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:113960800-113969600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:113960800-113974600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:113960800-113975000	Weak transcription	Liver	Liver
10	chr2:113962000-113969600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:113962200-113969000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:113962200-113969400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:113962200-113974800	Weak transcription	GM12878-XiMat	blood
14	chr2:113962600-113974600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:113964000-113969000	Weak transcription	Small Intestine	intestine
16	chr2:113964000-113972800	Enhancers	Fetal Kidney	kidney
17	chr2:113964600-113969800	Weak transcription	Pancreas	Pancrea
18	chr2:113964800-113969600	Weak transcription	Fetal Intestine Small	intestine
19	chr2:113965000-113969000	Weak transcription	Fetal Intestine Large	intestine
20	chr2:113966200-113969000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:113966200-113969000	Enhancers	Muscle Satellite Cultured Cells	--
22	chr2:113966200-113969000	Enhancers	HSMM	muscle
23	chr2:113966200-113969200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:113966200-113969800	Enhancers	Esophagus	oesophagus
25	chr2:113966200-113970400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:113966200-113972000	Enhancers	Fetal Stomach	stomach
27	chr2:113966800-113969400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:113967000-113970000	Enhancers	Colonic Mucosa	Colon
29	chr2:113967000-113970800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:113967200-113969000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr2:113967200-113971400	Enhancers	Placenta	Placenta
32	chr2:113967400-113969000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:113967400-113969000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:113967400-113969200	Enhancers	Stomach Smooth Muscle	stomach
35	chr2:113967400-113971200	Weak transcription	Thymus	Thymus
36	chr2:113967600-113975200	Weak transcription	Gastric	stomach
37	chr2:113967800-113969000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:113967800-113969200	Enhancers	Adipose Nuclei	Adipose
39	chr2:113967800-113970000	Enhancers	HMEC	breast
40	chr2:113968000-113969400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:113968200-113969000	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr2:113968200-113969800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:113968200-113970400	Enhancers	NHLF	lung
44	chr2:113968200-113970600	Enhancers	Left Ventricle	heart
45	chr2:113968200-113970800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:113968200-113970800	Enhancers	NHDF-Ad	bronchial
47	chr2:113968200-113973200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:113968200-113973200	Enhancers	HepG2	liver
49	chr2:113968400-113969000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:113968400-113969000	Enhancers	Monocytes-CD14+_RO01746	blood

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