Variant report

Variant	rs154340
Chromosome Location	chr14:79396590-79396591
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	chr14:79378742..79380336-chr14:79395070..79396642,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10873319	0.91[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap]
rs11159385	0.82[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs11159386	0.86[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs11159387	0.82[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs11159388	0.82[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs11159389	0.82[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs11159390	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs11845894	0.90[ASN][1000 genomes]
rs11847534	0.82[CHB][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs11847702	0.82[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs12050287	0.82[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs12588364	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs149088	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs150773	0.90[CEU][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs150774	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs154323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs154324	1.00[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs154329	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs154330	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs154333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs154334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs154336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs154343	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs154376	1.00[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap]
rs154378	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.96[MKK][hapmap];0.91[YRI][hapmap]
rs17108397	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs17108401	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17108405	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17108413	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs220103	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs220104	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2272292	0.82[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2272293	0.82[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs31349	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs31351	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs31352	0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs31424	0.84[JPT][hapmap]
rs31426	0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.82[ASN][1000 genomes]
rs31436	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs31437	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs31439	0.96[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs31441	0.82[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs31448	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs31450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3817535	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60746359	0.84[ASN][1000 genomes]
rs61330422	0.93[ASN][1000 genomes]
rs7142134	0.91[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap]
rs7157841	0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs8003966	0.86[ASN][1000 genomes]
rs8007109	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8007461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8008480	0.88[EUR][1000 genomes]
rs8011529	1.00[CHB][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832838	chr14:79306627-79445382	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv1048274	chr14:79323592-79417906	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv917249	chr14:79388181-79574717	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1041991	chr14:79394408-79644886	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs154340	TMED8	cis	parietal	SCAN
rs154340	NRXN3	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links