Variant report

Variant	rs28679654
Chromosome Location	chr2:113967617-113967618
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	TEAD4	chr2:113966638-113967926	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr2:113967589-113968540	ECC-1	luminal epithelium:	n/a	n/a
3	NFIC	chr2:113966541-113967649	ECC-1	luminal epithelium:	n/a	n/a
4	TCF12	chr2:113966727-113967640	ECC-1	luminal epithelium:	n/a	n/a
5	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: 19 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1015753	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1015755	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1049137	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1077855	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12472361	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2166421	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2289897	0.86[AMR][1000 genomes]
rs28522253	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2863242	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35222158	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35606997	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4849178	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4849180	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4849182	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6736334	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[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
rs28679654	AC016683.6	cis	Muscle Skeletal	GTEx
rs28679654	PAX8	cis	lung	GTEx
rs28679654	AC016683.6	cis	Whole Blood	GTEx
rs28679654	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs28679654	AC016683.6	cis	Artery Tibial	GTEx
rs28679654	PAX8	cis	Whole Blood	GTEx
rs28679654	AC016683.6	cis	lung	GTEx

Chromatin state (count:61 , 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	chr2:113960600-113975200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:113960800-113968600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr2:113960800-113969600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:113960800-113974600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:113960800-113975000	Weak transcription	Liver	Liver
14	chr2:113961000-113968400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr2:113962000-113969600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:113962200-113968400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:113962200-113969000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:113962200-113969400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:113962200-113974800	Weak transcription	GM12878-XiMat	blood
20	chr2:113962400-113968800	Weak transcription	Fetal Thymus	thymus
21	chr2:113962600-113974600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:113964000-113969000	Weak transcription	Small Intestine	intestine
23	chr2:113964000-113972800	Enhancers	Fetal Kidney	kidney
24	chr2:113964600-113969800	Weak transcription	Pancreas	Pancrea
25	chr2:113964800-113969600	Weak transcription	Fetal Intestine Small	intestine
26	chr2:113965000-113969000	Weak transcription	Fetal Intestine Large	intestine
27	chr2:113965800-113967800	Enhancers	HepG2	liver
28	chr2:113966200-113969000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:113966200-113969000	Enhancers	Muscle Satellite Cultured Cells	--
30	chr2:113966200-113969000	Enhancers	HSMM	muscle
31	chr2:113966200-113969200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:113966200-113969800	Enhancers	Esophagus	oesophagus
33	chr2:113966200-113970400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:113966200-113972000	Enhancers	Fetal Stomach	stomach
35	chr2:113966400-113967800	Enhancers	NHLF	lung
36	chr2:113966400-113968600	Enhancers	HSMMtube	muscle
37	chr2:113966400-113968800	Enhancers	Hela-S3	cervix
38	chr2:113966800-113968000	Enhancers	Lung	lung
39	chr2:113966800-113969400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:113967000-113968800	Enhancers	NHEK	skin
41	chr2:113967000-113970000	Enhancers	Colonic Mucosa	Colon
42	chr2:113967000-113970800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:113967200-113967800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:113967200-113967800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:113967200-113967800	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr2:113967200-113968200	Weak transcription	NHDF-Ad	bronchial
47	chr2:113967200-113968400	Weak transcription	NH-A	brain
48	chr2:113967200-113968400	Weak transcription	Osteobl	bone
49	chr2:113967200-113969000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr2:113967200-113971400	Enhancers	Placenta	Placenta

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