Variant report

Variant	rs12723149
Chromosome Location	chr1:79051989-79051990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11162508	1.00[ASN][1000 genomes]
rs12060353	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12065196	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12069538	1.00[ASN][1000 genomes]
rs12074883	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12731181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12737007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12743477	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12750516	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12751216	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17393482	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17397597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2057425	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2146490	0.80[EUR][1000 genomes]
rs34427371	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34491075	1.00[ASN][1000 genomes]
rs34635429	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34727624	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35153996	0.92[EUR][1000 genomes]
rs35223399	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35337590	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35735651	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35886379	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35922757	1.00[ASN][1000 genomes]
rs36037890	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36088152	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41309153	0.92[EUR][1000 genomes]
rs41313355	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67458600	0.80[EUR][1000 genomes]
rs71641401	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71643204	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71643205	0.91[EUR][1000 genomes]
rs7539356	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539847	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs899	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv830315	chr1:79008443-79200591	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1577	chr1:79013311-79058575	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12723149	TYW3	cis	cerebellum	SCAN
rs12723149	ST6GALNAC5	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79051400-79053600	Enhancers	HMEC	breast
2	chr1:79051600-79053200	Enhancers	HSMMtube	muscle
3	chr1:79051600-79053600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:79051600-79053600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:79051600-79053600	Enhancers	HSMM	muscle
6	chr1:79051800-79052400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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