Variant report

Variant	rs6718670
Chromosome Location	chr2:180643881-180643882
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	chr2:180635759..180637843-chr2:180643874..180645824,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10930884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10930885	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes]
rs1385970	1.00[CHB][hapmap]
rs1486232	1.00[CHB][hapmap]
rs165383	1.00[CHB][hapmap]
rs16867038	1.00[CHB][hapmap]
rs16867040	1.00[CHB][hapmap]
rs16867042	1.00[CHB][hapmap]
rs17772985	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs17773184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17773255	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17773308	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17773504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17773667	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17773899	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17773927	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17774379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17775571	1.00[CHB][hapmap]
rs17775913	1.00[CHB][hapmap]
rs17775991	1.00[CHB][hapmap]
rs17776109	1.00[CHB][hapmap]
rs17823821	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap]
rs17823881	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs17824301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs17824564	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17824691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17824733	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17824871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17824913	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17824948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825317	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17825747	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17831917	1.00[CHB][hapmap]
rs187744	1.00[CHB][hapmap]
rs2126424	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs2367798	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs2367800	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap]
rs2630544	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56342697	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56837904	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59847923	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60243803	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62180392	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62181524	1.00[ASN][1000 genomes]
rs62181526	1.00[ASN][1000 genomes]
rs6433805	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs6433806	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs6433808	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6727665	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs6738348	1.00[CHB][hapmap]
rs73046887	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046894	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046901	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7557892	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570042	1.00[CHB][hapmap]
rs7574741	1.00[CHB][hapmap]
rs7581371	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602719	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][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	nsv1002305	chr2:180568558-180812846	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428731	chr2:180629389-180805171	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6718670	HOXD9	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180634600-180644000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links