Variant report

Variant	rs28522253
Chromosome Location	chr2:113967387-113967388
allele	A/G
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	chr2:113966638-113967926	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr2:113966957-113967546	ECC-1	luminal epithelium:	n/a	n/a
3	NFIC	chr2:113966465-113967608	ECC-1	luminal epithelium:	n/a	n/a
4	NFIC	chr2:113966541-113967649	ECC-1	luminal epithelium:	n/a	n/a
5	TCF12	chr2:113966727-113967640	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr2:113966047-113968607	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113967235..113968789-chr2:113984371..113986823,2	MCF-7	breast:

Variant related genes	Relation type
PAX8-AS1	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1015753	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1015755	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1049137	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1077855	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12472361	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2166421	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2863242	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28679654	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35222158	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35606997	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4849178	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4849180	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4849182	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6736334	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv874900	chr2:113948378-113967990	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs28522253	AC016683.6	cis	Muscle Skeletal	GTEx
rs28522253	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs28522253	PAX8	cis	Whole Blood	GTEx
rs28522253	AC016683.6	cis	Whole Blood	GTEx
rs28522253	AC016683.6	cis	lung	GTEx
rs28522253	PAX8	cis	lung	GTEx
rs28522253	AC016683.6	cis	Artery Tibial	GTEx

Chromatin state (count:62 , 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	chr2:113957400-113967800	Weak transcription	Adipose Nuclei	Adipose
4	chr2:113957400-113969000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:113957400-113982600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:113958000-113975200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:113959200-113968800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:113959200-113968800	Weak transcription	K562	blood
9	chr2:113959600-113967600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:113960600-113975200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:113960800-113968600	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr2:113960800-113969600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:113960800-113974600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr2:113960800-113975000	Weak transcription	Liver	Liver
15	chr2:113961000-113968400	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr2:113962000-113969600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:113962200-113968400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:113962200-113969000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr2:113962200-113969400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:113962200-113974800	Weak transcription	GM12878-XiMat	blood
21	chr2:113962400-113968800	Weak transcription	Fetal Thymus	thymus
22	chr2:113962600-113974600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:113964000-113969000	Weak transcription	Small Intestine	intestine
24	chr2:113964000-113972800	Enhancers	Fetal Kidney	kidney
25	chr2:113964600-113969800	Weak transcription	Pancreas	Pancrea
26	chr2:113964800-113969600	Weak transcription	Fetal Intestine Small	intestine
27	chr2:113965000-113969000	Weak transcription	Fetal Intestine Large	intestine
28	chr2:113965800-113967800	Enhancers	HepG2	liver
29	chr2:113966200-113967600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:113966200-113969000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:113966200-113969000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr2:113966200-113969000	Enhancers	HSMM	muscle
33	chr2:113966200-113969200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:113966200-113969800	Enhancers	Esophagus	oesophagus
35	chr2:113966200-113970400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:113966200-113972000	Enhancers	Fetal Stomach	stomach
37	chr2:113966400-113967400	Enhancers	Fetal Lung	lung
38	chr2:113966400-113967400	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr2:113966400-113967800	Enhancers	NHLF	lung
40	chr2:113966400-113968600	Enhancers	HSMMtube	muscle
41	chr2:113966400-113968800	Enhancers	Hela-S3	cervix
42	chr2:113966600-113967400	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr2:113966600-113967400	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr2:113966600-113967400	Enhancers	Stomach Mucosa	stomach
45	chr2:113966800-113968000	Enhancers	Lung	lung
46	chr2:113966800-113969400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:113967000-113967400	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr2:113967000-113968800	Enhancers	NHEK	skin
49	chr2:113967000-113970000	Enhancers	Colonic Mucosa	Colon
50	chr2:113967000-113970800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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