Variant report

Variant	rs732778
Chromosome Location	chr2:74049341-74049342
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:74043930..74046271-chr2:74049022..74051900,2	K562	blood:
2	chr2:74048232..74053835-chr2:74054336..74058282,6	MCF-7	breast:
3	chr2:74046612..74048680-chr2:74048789..74050867,2	K562	blood:
4	chr2:74048023..74052470-chr2:74054588..74058277,4	K562	blood:
5	chr2:74048452..74051590-chr2:74209610..74212844,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235499	Chromatin interaction
ENSG00000124356	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10172044	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10191988	0.85[EUR][1000 genomes]
rs10193032	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10203740	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10208995	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11126415	0.82[EUR][1000 genomes]
rs11126416	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11126417	0.87[EUR][1000 genomes]
rs11891140	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11892172	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11894953	0.85[EUR][1000 genomes]
rs12052539	0.82[EUR][1000 genomes]
rs12053242	0.82[EUR][1000 genomes]
rs12615807	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12624267	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12713789	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12713790	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12713791	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12713793	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12713794	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12713795	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12713797	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12713798	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12992607	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13003035	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13006598	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13020517	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13033744	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13383097	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17350125	0.82[EUR][1000 genomes]
rs17350188	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1806683	0.83[EUR][1000 genomes]
rs1815028	0.83[EUR][1000 genomes]
rs2006997	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2116367	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2272051	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2272178	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2421557	0.83[EUR][1000 genomes]
rs2421558	0.82[EUR][1000 genomes]
rs2421559	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2421672	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2421674	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2421675	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2421676	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2421677	0.83[EUR][1000 genomes]
rs2462127	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35498419	0.82[EUR][1000 genomes]
rs35791379	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3813228	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3980695	0.83[EUR][1000 genomes]
rs4241257	0.83[EUR][1000 genomes]
rs4358149	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4852316	0.81[EUR][1000 genomes]
rs4852976	0.82[EUR][1000 genomes]
rs4852977	0.83[EUR][1000 genomes]
rs4852978	0.84[EUR][1000 genomes]
rs6748233	0.83[EUR][1000 genomes]
rs6749841	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6750494	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6750515	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6750877	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6755500	0.84[EUR][1000 genomes]
rs7210	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7558546	0.82[EUR][1000 genomes]
rs7591112	0.85[EUR][1000 genomes]
rs7597302	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7599453	0.82[EUR][1000 genomes]
rs891695	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs891696	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9309475	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9309476	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv834260	chr2:73906106-74076520	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv2780	chr2:73994168-74057248	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs732778	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs732778	ALMS1P	cis	Nerve Tibial	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74048400-74049400	Flanking Active TSS	GM12878-XiMat	blood
2	chr2:74048800-74054800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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