Variant report

Variant	rs354239
Chromosome Location	chr2:54954824-54954825
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1848923	0.90[ASN][1000 genomes]
rs241662	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2567837	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2666036	0.83[AFR][1000 genomes]
rs354188	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs354191	0.85[AFR][1000 genomes]
rs354193	0.96[AFR][1000 genomes]
rs354215	0.81[EUR][1000 genomes]
rs354241	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs354242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671229	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs72618666	0.89[ASN][1000 genomes]
rs72618669	0.90[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	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1005449	chr2:54938633-55129503	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv2622685	chr2:54953935-54955417	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs354239	EML6	cis	Artery Tibial	GTEx
rs354239	EML6	cis	Esophagus Muscularis	GTEx
rs354239	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL
rs354239	EML6	cis	Artery Aorta	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54952600-54955400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:54952600-54955600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:54952800-54955200	Weak transcription	HSMM	muscle
4	chr2:54953200-54955000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:54953400-54955400	Weak transcription	HSMMtube	muscle
6	chr2:54953600-54956600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:54954200-54955400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:54954400-54955400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:54954400-54955400	Weak transcription	Hela-S3	cervix
10	chr2:54954400-54955400	Weak transcription	HMEC	breast
11	chr2:54954400-54955400	Weak transcription	NHEK	skin
12	chr2:54954600-54958600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:54954600-54965000	Weak transcription	Fetal Intestine Small	intestine
14	chr2:54954800-54956800	Enhancers	HepG2	liver

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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