Variant report

Variant	rs2002510
Chromosome Location	chr2:114061466-114061467
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10864913	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11123176	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11123177	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11123179	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11685107	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11685421	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11695071	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475140	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12476056	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12476331	0.81[AMR][1000 genomes]
rs13015130	0.83[AMR][1000 genomes]
rs36000169	0.89[AMR][1000 genomes]
rs6716573	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs7425070	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv874901	chr2:114022569-114079565	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv998204	chr2:114023917-114075446	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv961872	chr2:114041837-114061641	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2762785	chr2:114044712-114081784	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2002510	AC016683.6	cis	lung	GTEx
rs2002510	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs2002510	PAX8	cis	lung	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114055000-114062400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:114058200-114067200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:114060600-114062400	Weak transcription	Fetal Muscle Leg	muscle
4	chr2:114060800-114062400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:114060800-114065400	Weak transcription	Gastric	stomach
6	chr2:114061000-114062400	Weak transcription	HSMMtube	muscle
7	chr2:114061200-114062800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:114061200-114064200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:114061400-114062600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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