Variant report

Variant	rs1518759
Chromosome Location	chr2:128182375-128182376
allele	G/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	POLR2A	chr2:128182272-128188076	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:128143841..128146885-chr2:128179410..128184717,5	MCF-7	breast:

Variant related genes	Relation type
MIR4783	TF binding region
ENSG00000169967	Chromatin interaction
ENSG00000236682	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12151780	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12463538	0.92[ASN][1000 genomes]
rs12464295	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12468304	0.97[ASN][1000 genomes]
rs12476767	0.92[ASN][1000 genomes]
rs12478656	0.92[ASN][1000 genomes]
rs12989081	0.83[EUR][1000 genomes]
rs13001648	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1401296	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1799808	0.87[ASN][1000 genomes]
rs1967425	0.98[ASN][1000 genomes]
rs2069912	0.89[ASN][1000 genomes]
rs2069914	0.88[ASN][1000 genomes]
rs2069915	0.87[ASN][1000 genomes]
rs2069920	0.92[ASN][1000 genomes]
rs2069921	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2069924	0.99[ASN][1000 genomes]
rs2069931	0.98[ASN][1000 genomes]
rs2069933	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4662729	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4662730	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5936	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62160290	0.88[ASN][1000 genomes]
rs6710535	0.98[ASN][1000 genomes]
rs6728362	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6749002	0.92[ASN][1000 genomes]
rs6754772	0.94[ASN][1000 genomes]
rs6754999	0.93[ASN][1000 genomes]
rs971207	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs973760	0.87[AMR][1000 genomes];0.92[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	nsv583036	chr2:128173819-128183914	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv875013	chr2:128177974-128183145	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1518759	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs1518759	AC068282.3	cis	Muscle Skeletal	GTEx
rs1518759	AC068282.3	cis	Stomach	GTEx
rs1518759	AC068282.3	cis	Thyroid	GTEx
rs1518759	AC068282.3	cis	Whole Blood	GTEx
rs1518759	AC068282.3	cis	Heart Left Ventricle	GTEx
rs1518759	AC068282.3	cis	lung	GTEx
rs1518759	AC068282.3	cis	Artery Tibial	GTEx
rs1518759	AC068282.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128180200-128186800	Strong transcription	Liver	Liver
2	chr2:128181000-128191000	Weak transcription	Aorta	Aorta
3	chr2:128181400-128182400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:128181400-128185200	Weak transcription	Spleen	Spleen
5	chr2:128181400-128186200	Weak transcription	Esophagus	oesophagus
6	chr2:128181400-128194000	Weak transcription	Gastric	stomach
7	chr2:128181400-128195200	Weak transcription	Pancreas	Pancrea
8	chr2:128181400-128196000	Weak transcription	Lung	lung
9	chr2:128181400-128209800	Weak transcription	Right Atrium	heart
10	chr2:128181600-128182400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:128181600-128182800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr2:128181600-128182800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:128181600-128183000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:128181600-128183000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:128181600-128185200	Weak transcription	Fetal Intestine Small	intestine
16	chr2:128181600-128187600	Strong transcription	HepG2	liver
17	chr2:128181600-128195000	Weak transcription	Fetal Intestine Large	intestine
18	chr2:128181600-128197200	Weak transcription	Brain Anterior Caudate	brain
19	chr2:128181800-128182600	Weak transcription	A549	lung

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