Variant report

Variant	rs354232
Chromosome Location	chr2:54916910-54916911
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54784126..54785998-chr2:54916607..54919364,2	K562	blood:
2	chr2:54783616..54785998-chr2:54916607..54919364,3	K562	blood:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10170355	0.89[CHB][hapmap]
rs10175967	0.87[ASN][1000 genomes]
rs10176359	0.89[CHB][hapmap]
rs10176445	0.89[CHB][hapmap]
rs10182836	0.89[CHB][hapmap]
rs10183867	0.89[CHB][hapmap]
rs10184128	0.89[CHB][hapmap]
rs10188185	0.85[CHB][hapmap];0.85[JPT][hapmap];0.98[ASN][1000 genomes]
rs10193692	0.88[CHB][hapmap]
rs10205410	0.86[CHB][hapmap]
rs10206143	0.89[CHB][hapmap]
rs1137645	0.89[CHB][hapmap]
rs11883962	0.88[ASN][1000 genomes]
rs11892236	0.84[CHB][hapmap]
rs11892443	0.87[CHB][hapmap]
rs11902987	0.89[CHB][hapmap]
rs12713264	0.89[CHB][hapmap]
rs12713265	0.89[CHB][hapmap]
rs12713268	0.89[CHB][hapmap]
rs12713269	0.89[CHB][hapmap]
rs12713273	0.89[CHB][hapmap]
rs12713275	0.88[AFR][1000 genomes]
rs12713276	0.85[ASN][1000 genomes]
rs13386146	0.89[CHB][hapmap]
rs13391522	0.89[CHB][hapmap]
rs13391803	0.88[CHB][hapmap]
rs13399656	0.88[CHB][hapmap]
rs13403284	0.89[CHB][hapmap]
rs13428703	0.86[GIH][hapmap]
rs17045939	0.89[CHB][hapmap]
rs17046257	0.89[CHB][hapmap];0.90[ASN][1000 genomes]
rs2229503	0.89[CHB][hapmap]
rs241661	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2567834	0.86[EUR][1000 genomes]
rs3287	0.89[CHB][hapmap]
rs34456795	0.96[ASN][1000 genomes]
rs354222	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs354225	0.81[ASN][1000 genomes]
rs3739109	0.88[CHB][hapmap]
rs3796019	0.89[CHB][hapmap]
rs4346422	0.89[CHB][hapmap]
rs4455200	0.88[CHB][hapmap]
rs4671969	0.91[AFR][1000 genomes]
rs6545430	0.89[CHB][hapmap]
rs6545435	0.89[CHB][hapmap]
rs6545438	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs6706263	0.88[CHB][hapmap]
rs6708082	0.81[GIH][hapmap]
rs6734445	0.89[CHB][hapmap]
rs6734536	0.89[CHB][hapmap]
rs6744586	0.87[ASN][1000 genomes]
rs6752720	0.86[GIH][hapmap]
rs67909358	0.88[ASN][1000 genomes]
rs7340302	0.89[CHB][hapmap]
rs7556752	0.89[CHB][hapmap]
rs7569127	0.89[CHB][hapmap]
rs7584223	0.89[CHB][hapmap]
rs7587575	0.90[YRI][hapmap]
rs7599241	0.89[CHB][hapmap]
rs7608414	0.89[CHB][hapmap]
rs9917248	0.94[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	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	nsv963149	chr2:54914350-54920863	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs354232	EML6	cis	Thyroid	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54908800-54921400	Weak transcription	Lung	lung
2	chr2:54911000-54918600	Weak transcription	HepG2	liver
3	chr2:54911000-54919000	Weak transcription	Pancreas	Pancrea
4	chr2:54915200-54918800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:54915400-54918800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:54915600-54918800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:54916200-54919000	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links