Variant report

Variant	rs7726732
Chromosome Location	chr5:56977231-56977232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:56977051..56979495-chr5:56982017..56985832,3	MCF-7	breast:
2	chr5:56961466..56964458-chr5:56975327..56978109,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPBP1-3	chr5:56976800-56977304	NONHSAT101585

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10057570	0.93[AFR][1000 genomes]
rs10057880	1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10069403	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10072292	1.00[YRI][hapmap]
rs10077005	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10487613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10940569	0.87[EUR][1000 genomes]
rs10940570	0.84[EUR][1000 genomes]
rs11738377	0.87[EUR][1000 genomes]
rs11738862	0.87[EUR][1000 genomes]
rs11740506	0.87[EUR][1000 genomes]
rs11742166	0.87[EUR][1000 genomes]
rs12153161	0.86[EUR][1000 genomes]
rs12520986	1.00[AFR][1000 genomes]
rs12652614	0.86[EUR][1000 genomes]
rs13161204	0.87[EUR][1000 genomes]
rs13177900	0.86[EUR][1000 genomes]
rs13185580	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1347071	1.00[YRI][hapmap]
rs1476831	0.87[EUR][1000 genomes]
rs1476832	0.87[EUR][1000 genomes]
rs170740	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs170741	0.93[AFR][1000 genomes]
rs1821210	0.87[MKK][hapmap];1.00[YRI][hapmap]
rs183477	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1861052	0.81[AFR][1000 genomes]
rs1861059	1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs2017201	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2041678	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2161500	0.81[AFR][1000 genomes]
rs2191445	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2191446	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2191448	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2191449	0.87[EUR][1000 genomes]
rs2215420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215421	0.85[EUR][1000 genomes]
rs229960	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs229961	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs229963	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs229965	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs230823	0.85[EUR][1000 genomes]
rs230824	0.84[EUR][1000 genomes]
rs230825	0.84[EUR][1000 genomes]
rs230826	0.84[EUR][1000 genomes]
rs230827	0.83[EUR][1000 genomes]
rs230846	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230847	0.85[EUR][1000 genomes]
rs230848	0.85[EUR][1000 genomes]
rs230849	0.85[EUR][1000 genomes]
rs230850	0.85[EUR][1000 genomes]
rs230851	0.85[EUR][1000 genomes]
rs230852	0.85[EUR][1000 genomes]
rs230853	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230854	0.87[EUR][1000 genomes]
rs230855	0.87[EUR][1000 genomes]
rs230856	0.87[EUR][1000 genomes]
rs230857	0.86[EUR][1000 genomes]
rs230858	0.86[EUR][1000 genomes]
rs230859	0.86[EUR][1000 genomes]
rs230860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2408846	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2408849	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2408850	0.86[AFR][1000 genomes]
rs2408854	0.87[MKK][hapmap];1.00[YRI][hapmap]
rs2568537	1.00[YRI][hapmap]
rs2898028	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4141128	0.85[EUR][1000 genomes]
rs4235474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4285175	0.87[MKK][hapmap]
rs4508990	0.86[AFR][1000 genomes]
rs4699909	0.87[EUR][1000 genomes]
rs4699910	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4699913	0.87[MKK][hapmap];1.00[YRI][hapmap]
rs4700210	0.86[EUR][1000 genomes]
rs4700211	0.87[EUR][1000 genomes]
rs4700214	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4700233	0.87[MKK][hapmap];1.00[YRI][hapmap]
rs6450430	0.99[EUR][1000 genomes]
rs6450431	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6866242	0.86[AFR][1000 genomes]
rs6886241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs702695	0.85[EUR][1000 genomes]
rs702696	0.85[EUR][1000 genomes]
rs7714534	0.87[EUR][1000 genomes]
rs7719947	0.87[EUR][1000 genomes]
rs7732108	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7737409	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs854036	1.00[YRI][hapmap]
rs854137	0.85[EUR][1000 genomes]
rs887503	0.87[EUR][1000 genomes]
rs917655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986101	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs991727	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]

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	nsv830309	chr5:56837590-56978283	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7726732	TADA2B	trans	parietal	SCAN
rs7726732	GZMK	cis	cerebellum	SCAN
rs7726732	CDC20B	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:56972400-56978400	Weak transcription	Ovary	ovary
2	chr5:56972400-56988400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr5:56973400-56980000	Weak transcription	Liver	Liver
4	chr5:56975400-56979200	Weak transcription	K562	blood
5	chr5:56976200-56980600	Enhancers	HMEC	breast
6	chr5:56976600-56978800	Enhancers	NHEK	skin
7	chr5:56976600-56981200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:56976800-56978200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:56977200-56978200	Enhancers	NH-A	brain
10	chr5:56977200-56979000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:56977200-56979400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:56977200-56979800	Enhancers	Hela-S3	cervix

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