Variant report

Variant	rs494863
Chromosome Location	chr15:43502302-43502303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43480701..43484189-chr15:43499859..43502784,3	K562	blood:
2	chr15:43500155..43503014-chr15:43621772..43625357,3	K562	blood:
3	chr15:43498126..43499965-chr15:43501635..43503174,2	K562	blood:
4	chr15:43500986..43502803-chr15:43507049..43508865,2	K562	blood:

Variant related genes	Relation type
ENSG00000166947	Chromatin interaction
ENSG00000168803	Chromatin interaction
ENSG00000168806	Chromatin interaction
ENSG00000166946	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11070386	0.89[CEU][hapmap];0.94[CHB][hapmap]
rs11070391	0.89[CEU][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs11070396	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070397	0.86[EUR][1000 genomes]
rs11070398	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11630595	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs11855754	1.00[CEU][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12592725	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12899266	0.89[CEU][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1462856	0.89[CEU][hapmap]
rs16957511	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1834643	0.92[EUR][1000 genomes]
rs2042742	0.94[EUR][1000 genomes]
rs2241516	1.00[CEU][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2412752	0.95[CHB][hapmap];0.89[CHD][hapmap]
rs28585036	0.86[CEU][hapmap]
rs28756768	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2899077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2947019	1.00[CEU][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34646108	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3784267	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3784268	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4573908	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs4924704	0.89[CEU][hapmap]
rs4924709	0.80[ASN][1000 genomes]
rs495286	1.00[CEU][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs497138	1.00[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs499280	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs530305	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs531850	1.00[CEU][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs538218	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs540587	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493076	0.89[CEU][hapmap]
rs6493077	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap]
rs7174915	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs7183814	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8027371	0.86[CHD][hapmap];0.94[JPT][hapmap]
rs8027733	0.89[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap]

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	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs494863	TGM5	cis	lymphoblastoid	seeQTL
rs494863	CCNDBP1	cis	Lymphoblastoid	GTEx
rs494863	CCNDBP1	cis	lymphoblastoid	seeQTL
rs494863	ARV1	trans	lymphoblastoid	seeQTL
rs494863	CCNDBP1	Cis_1M	lymphoblastoid	RTeQTL
rs494863	CCNDBP1	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43489800-43503000	Weak transcription	K562	blood
2	chr15:43489800-43513200	Weak transcription	Right Atrium	heart
3	chr15:43500600-43503000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:43501600-43511000	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links