Variant report

Variant	rs4848323
Chromosome Location	chr2:114032767-114032768
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10864911	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10864912	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12478858	0.83[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1446245	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446246	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1466018	0.81[CEU][hapmap];0.87[MEX][hapmap]
rs6542127	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs708633	0.81[CEU][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.85[AMR][1000 genomes]
rs7560701	0.83[MEX][hapmap]
rs877201	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs895415	0.81[CEU][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.85[AMR][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	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	nsv535895	chr2:114015492-114037018	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4848323	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs4848323	LOC654433	cis	parietal	SCAN
rs4848323	PAX8	cis	parietal	SCAN
rs4848323	AC016683.6	cis	Artery Tibial	GTEx
rs4848323	AC016683.6	cis	Whole Blood	GTEx
rs4848323	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs4848323	AC016683.6	cis	Muscle Skeletal	GTEx
rs4848323	LOC654433	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114023200-114039800	Weak transcription	Gastric	stomach
2	chr2:114026600-114033400	Weak transcription	Lung	lung
3	chr2:114026600-114034400	Weak transcription	Pancreas	Pancrea
4	chr2:114030200-114033000	Enhancers	A549	lung
5	chr2:114030200-114033400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:114031600-114037000	Bivalent/Poised TSS	Fetal Kidney	kidney
7	chr2:114032200-114034400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:114032600-114035000	Weak transcription	Right Atrium	heart

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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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