Variant report

Variant	rs4671984
Chromosome Location	chr2:55095145-55095146
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55091369..55092932-chr2:55094954..55097133,2	K562	blood:
2	chr2:55094613..55097035-chr2:55109267..55110940,2	K562	blood:
3	chr2:55001781..55004496-chr2:55092891..55095421,2	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10179594	0.82[CHB][hapmap]
rs10196667	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs10432676	0.94[ASN][1000 genomes]
rs10432677	0.97[ASN][1000 genomes]
rs10746530	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11125551	0.81[JPT][hapmap]
rs12052579	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1371019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17417648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2116491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2920897	0.82[CHB][hapmap]
rs2968789	0.82[CHB][hapmap]
rs4671980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4671983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57401377	0.88[ASN][1000 genomes]
rs6545462	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs73938635	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv1796192	chr2:55081033-55110969	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4671984	RTN4	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55068400-55096200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:55068400-55109000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:55068600-55122400	Weak transcription	Brain Anterior Caudate	brain
4	chr2:55078800-55106800	Weak transcription	Brain Angular Gyrus	brain
5	chr2:55081400-55122400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:55087000-55098600	Weak transcription	HepG2	liver
7	chr2:55087800-55126000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr2:55088000-55096000	Weak transcription	Psoas Muscle	Psoas
9	chr2:55088200-55098800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:55092000-55098800	Weak transcription	Liver	Liver
11	chr2:55092400-55111000	Weak transcription	Pancreas	Pancrea
12	chr2:55093000-55097000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:55093800-55095200	Enhancers	Primary B cells from peripheral blood	blood
14	chr2:55093800-55095200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr2:55093800-55095800	Enhancers	Primary B cells from cord blood	blood
16	chr2:55094000-55098600	Weak transcription	HSMM	muscle
17	chr2:55094200-55095200	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr2:55094200-55098000	Weak transcription	HSMMtube	muscle
19	chr2:55094200-55098800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:55094400-55098400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:55094800-55095400	Enhancers	GM12878-XiMat	blood
22	chr2:55094800-55096200	Weak transcription	Esophagus	oesophagus

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