Variant report

Variant	rs17046413
Chromosome Location	chr2:55071861-55071862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17046514	0.83[GIH][hapmap];0.83[TSI][hapmap]
rs4671232	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4671978	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4671981	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4671982	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4671993	0.88[GIH][hapmap];0.91[TSI][hapmap]
rs6716399	0.87[ASN][1000 genomes]
rs723975	0.89[AMR][1000 genomes];0.81[EUR][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	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	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
3	esv1844727	chr2:54999712-55084583	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv874153	chr2:55042463-55073428	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv874154	chr2:55063113-55084583	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17046413	RTN4	cis	frontal cortex	BrainEAC
rs17046413	RTN4	cis	brain	BrainEAC
rs17046413	EML6	cis	brain	BrainEAC

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55053400-55079000	Weak transcription	HepG2	liver
2	chr2:55063800-55072800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:55066400-55072400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:55066800-55084400	Weak transcription	HSMMtube	muscle
5	chr2:55066800-55088800	Weak transcription	Brain Substantia Nigra	brain
6	chr2:55067200-55072200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:55068400-55096200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:55068400-55109000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:55068600-55072000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:55068600-55122400	Weak transcription	Brain Anterior Caudate	brain
11	chr2:55068800-55072600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:55070400-55077200	Weak transcription	NHEK	skin
13	chr2:55071200-55074600	Weak transcription	Pancreas	Pancrea
14	chr2:55071800-55073400	Enhancers	Primary B cells from cord blood	blood
15	chr2:55071800-55073400	Enhancers	Primary B cells from peripheral blood	blood

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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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