Variant report

Variant	rs17046149
Chromosome Location	chr2:54910872-54910873
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54899732..54901951-chr2:54909870..54911861,2	MCF-7	breast:
2	chr2:54907957..54910043-chr2:54910399..54913105,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10169439	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs10170355	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10175967	0.87[EUR][1000 genomes]
rs10176359	1.00[CHB][hapmap]
rs10176445	1.00[CHB][hapmap]
rs10182836	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10183867	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10184128	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10188185	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10193692	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10194108	0.81[EUR][1000 genomes]
rs10205410	1.00[CHB][hapmap]
rs10206143	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10528	0.85[CEU][hapmap];0.88[CHB][hapmap]
rs1137645	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11883962	0.82[EUR][1000 genomes]
rs11892236	1.00[CHB][hapmap]
rs11892443	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11902987	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11904679	0.89[CHB][hapmap]
rs12713264	1.00[CHB][hapmap]
rs12713265	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12713268	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12713269	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12713273	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12713276	0.86[EUR][1000 genomes]
rs13021615	0.88[CHB][hapmap]
rs13386146	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13391522	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13391803	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13399656	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13403284	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13428703	0.86[GIH][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs17039558	0.89[CHB][hapmap]
rs17045939	1.00[CHB][hapmap]
rs17046077	0.93[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs17046097	0.86[JPT][hapmap]
rs17046108	0.93[CEU][hapmap];0.88[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[ASN][1000 genomes]
rs17046257	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs2048370	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2229503	1.00[CHB][hapmap]
rs2271329	0.93[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap]
rs241661	0.85[ASN][1000 genomes]
rs3287	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs33946849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34456795	0.89[EUR][1000 genomes]
rs354225	0.83[ASN][1000 genomes]
rs354232	0.89[CHB][hapmap];0.81[GIH][hapmap]
rs3739109	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3796019	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3796022	0.89[CHB][hapmap]
rs3850350	0.83[AMR][1000 genomes]
rs4261758	0.89[CHB][hapmap]
rs4319969	0.89[CHB][hapmap]
rs4346422	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4455200	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6545430	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6545435	1.00[CHB][hapmap]
rs6706263	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6708082	1.00[GIH][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs6734445	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6734536	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6740110	0.84[EUR][1000 genomes]
rs6744586	0.82[EUR][1000 genomes]
rs6752720	0.86[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs6753004	0.82[EUR][1000 genomes]
rs67909358	0.82[EUR][1000 genomes]
rs7340302	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs7556752	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7569127	1.00[CHB][hapmap]
rs7584223	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs7599241	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7608414	1.00[CHB][hapmap]
rs9917248	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17046149	EML6	cis	Thyroid	GTEx
rs17046149	RPL23AP32	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54903400-54915600	Weak transcription	Right Atrium	heart
2	chr2:54908000-54914800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:54908200-54914800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:54908800-54921400	Weak transcription	Lung	lung
5	chr2:54910200-54911000	Enhancers	HepG2	liver
6	chr2:54910600-54911000	Enhancers	NHEK	skin
7	chr2:54910800-54911000	Enhancers	Pancreas	Pancrea
8	chr2:54910800-54911200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr2:54910800-54911400	Enhancers	Fetal Intestine Large	intestine
10	chr2:54910800-54911400	Enhancers	HMEC	breast

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