Variant report

Variant	rs2303747
Chromosome Location	chr5:114977828-114977829
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:114970889..114973875-chr5:114975413..114978406,3	MCF-7	breast:
2	chr5:114976334..114978260-chr5:115174863..115176916,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMED7-1	chr5:114977822-114977993	NR_104674

Variant related genes	Relation type
ENSG00000145782	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10055677	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10057920	0.81[ASN][1000 genomes]
rs10080011	0.81[ASN][1000 genomes]
rs10080133	0.81[ASN][1000 genomes]
rs11241332	0.81[ASN][1000 genomes]
rs11738797	0.81[ASN][1000 genomes]
rs11738951	0.80[ASN][1000 genomes]
rs11742196	0.81[ASN][1000 genomes]
rs12653456	0.81[ASN][1000 genomes]
rs12655570	0.81[ASN][1000 genomes]
rs12655606	0.81[ASN][1000 genomes]
rs12655651	0.80[ASN][1000 genomes]
rs13156452	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13163433	0.81[ASN][1000 genomes]
rs13164059	0.81[ASN][1000 genomes]
rs13164545	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13183738	0.81[ASN][1000 genomes]
rs13186296	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs171774	0.92[CEU][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs2270930	0.81[ASN][1000 genomes]
rs256942	0.92[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs256944	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs256945	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs256947	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs256948	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs256949	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs256950	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs256951	0.92[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs256952	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs256953	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs256954	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs256962	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs256964	0.92[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs256967	0.87[EUR][1000 genomes]
rs256969	0.87[EUR][1000 genomes]
rs256988	0.87[EUR][1000 genomes]
rs256991	0.87[EUR][1000 genomes]
rs256993	0.87[EUR][1000 genomes]
rs256997	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs256998	0.88[EUR][1000 genomes]
rs35010823	0.81[ASN][1000 genomes]
rs377290	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3822579	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs400570	0.96[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs413059	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs415577	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs424434	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs428191	0.82[CHB][hapmap]
rs4920875	0.81[ASN][1000 genomes]
rs4920967	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4920969	0.98[ASN][1000 genomes]
rs4920976	0.81[ASN][1000 genomes]
rs4920977	0.81[ASN][1000 genomes]
rs4920978	0.81[ASN][1000 genomes]
rs4920982	0.81[ASN][1000 genomes]
rs698365	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs698366	0.89[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs698367	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs716515	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7702283	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7702869	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7702881	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7723429	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7727624	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs790824	0.81[CHB][hapmap]
rs790825	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9326969	0.82[CHB][hapmap];0.83[CHD][hapmap]

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	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2303747	SEMA6A	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114976200-114978800	Weak transcription	Liver	Liver
2	chr5:114977600-114978000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:114977600-114978000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:114977600-114978000	Enhancers	Osteobl	bone
5	chr5:114977800-114978200	Enhancers	HUVEC	blood vessel

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