Variant report

Variant	rs917655
Chromosome Location	chr5:56979513-56979514
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	chr5:56978767..56981076-chr5:56987149..56990064,2	K562	blood:

Extended variants
information (count: 99 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:97)

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];0.83[EUR][1000 genomes]
rs10072292	1.00[YRI][hapmap]
rs10077005	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10487613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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	0.86[EUR][1000 genomes]
rs10940570	0.85[EUR][1000 genomes]
rs11738377	0.86[EUR][1000 genomes]
rs11738862	0.87[EUR][1000 genomes]
rs11740506	0.86[EUR][1000 genomes]
rs11742166	0.86[EUR][1000 genomes]
rs12153161	0.87[EUR][1000 genomes]
rs12520986	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12652614	0.87[EUR][1000 genomes]
rs13161204	0.86[EUR][1000 genomes]
rs13177900	0.85[EUR][1000 genomes]
rs13185580	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1347071	1.00[YRI][hapmap]
rs1476831	0.86[EUR][1000 genomes]
rs1476832	0.86[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];0.92[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]
rs2191444	0.81[EUR][1000 genomes]
rs2191445	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2191446	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2191448	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2191449	0.86[EUR][1000 genomes]
rs2215420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215421	0.84[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];0.82[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	0.85[EUR][1000 genomes]
rs230825	0.85[EUR][1000 genomes]
rs230826	0.85[EUR][1000 genomes]
rs230827	0.84[EUR][1000 genomes]
rs230846	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230847	0.86[EUR][1000 genomes]
rs230848	0.86[EUR][1000 genomes]
rs230849	0.86[EUR][1000 genomes]
rs230850	0.86[EUR][1000 genomes]
rs230851	0.86[EUR][1000 genomes]
rs230852	0.86[EUR][1000 genomes]
rs230853	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230854	0.86[EUR][1000 genomes]
rs230855	0.86[EUR][1000 genomes]
rs230856	0.86[EUR][1000 genomes]
rs230857	0.87[EUR][1000 genomes]
rs230858	0.87[EUR][1000 genomes]
rs230859	0.87[EUR][1000 genomes]
rs230860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2408846	0.94[AMR][1000 genomes];0.92[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4285175	0.87[MKK][hapmap]
rs4458541	0.87[MKK][hapmap];1.00[YRI][hapmap]
rs4508990	0.86[AFR][1000 genomes]
rs4699909	0.86[EUR][1000 genomes]
rs4699910	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4699913	0.87[MKK][hapmap];1.00[YRI][hapmap]
rs4700210	0.87[EUR][1000 genomes]
rs4700211	0.86[EUR][1000 genomes]
rs4700214	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4700233	0.87[MKK][hapmap];1.00[YRI][hapmap]
rs6450430	0.98[EUR][1000 genomes]
rs6450431	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6866242	0.86[AFR][1000 genomes]
rs6886241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs702695	0.86[EUR][1000 genomes]
rs702696	0.86[EUR][1000 genomes]
rs7714534	0.86[EUR][1000 genomes]
rs7719947	0.86[EUR][1000 genomes]
rs7726732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732108	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7737409	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs854036	1.00[YRI][hapmap]
rs854137	0.86[EUR][1000 genomes]
rs887503	0.86[EUR][1000 genomes]
rs986101	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs991727	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[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	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
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs917655	TADA2B	trans	parietal	SCAN
rs917655	GZMK	cis	cerebellum	SCAN
rs917655	CDC20B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:56972400-56988400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr5:56973400-56980000	Weak transcription	Liver	Liver
3	chr5:56976200-56980600	Enhancers	HMEC	breast
4	chr5:56976600-56981200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:56977200-56979800	Enhancers	Hela-S3	cervix
6	chr5:56978400-56980400	Enhancers	Ovary	ovary
7	chr5:56978800-56983600	Weak transcription	NHEK	skin
8	chr5:56979000-56979800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr5:56979200-56979600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr5:56979200-56979600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:56979200-56979600	Enhancers	K562	blood
12	chr5:56979400-56983600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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