Variant report

Variant	rs241662
Chromosome Location	chr2:54953036-54953037
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1848923	0.90[ASN][1000 genomes]
rs2567837	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs354188	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs354191	0.81[AFR][1000 genomes]
rs354193	0.91[AFR][1000 genomes]
rs354239	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354241	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs354242	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671229	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	esv3362527	chr2:54951248-54953146	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs241662	EML6	cis	Esophagus Muscularis	GTEx
rs241662	EML6	cis	Artery Aorta	GTEx
rs241662	EML6	cis	Artery Tibial	GTEx
rs241662	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54950000-54953400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr2:54950200-54953200	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr2:54950200-54953400	Active TSS	Brain Cingulate Gyrus	brain
4	chr2:54950200-54953600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:54950200-54954400	Active TSS	Brain Angular Gyrus	brain
6	chr2:54950400-54954000	Active TSS	Fetal Brain Female	brain
7	chr2:54951800-54953800	Weak transcription	Hela-S3	cervix
8	chr2:54952000-54953200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
9	chr2:54952400-54953200	Flanking Active TSS	Brain Anterior Caudate	brain
10	chr2:54952400-54953400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
11	chr2:54952600-54953200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
12	chr2:54952600-54953200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:54952600-54953200	Bivalent Enhancer	Brain Germinal Matrix	brain
14	chr2:54952600-54953200	Flanking Active TSS	HSMMtube	muscle
15	chr2:54952600-54953400	Enhancers	Brain Substantia Nigra	brain
16	chr2:54952600-54955400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:54952600-54955600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:54952800-54953200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:54952800-54953400	Enhancers	HepG2	liver
20	chr2:54952800-54955200	Weak transcription	HSMM	muscle
21	chr2:54953000-54953200	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
22	chr2:54953000-54953400	Flanking Bivalent TSS/Enh	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links