Variant report

Variant	rs2408849
Chromosome Location	chr5:57029268-57029269
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10057570	0.93[AFR][1000 genomes]
rs10057880	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10063185	1.00[ASN][1000 genomes]
rs10069403	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10072292	1.00[YRI][hapmap]
rs10077005	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487613	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10487614	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10940575	1.00[ASN][1000 genomes]
rs12520986	1.00[AFR][1000 genomes]
rs13162397	1.00[ASN][1000 genomes]
rs13185580	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1347071	1.00[YRI][hapmap]
rs170740	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs170741	0.93[AFR][1000 genomes]
rs1821210	0.87[MKK][hapmap];1.00[YRI][hapmap]
rs183477	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1861052	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1861059	1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs2017201	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2041677	1.00[ASN][1000 genomes]
rs2041678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2161500	0.81[AFR][1000 genomes]
rs2191444	0.84[EUR][1000 genomes]
rs2191445	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2191446	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2191448	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2215420	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs229960	1.00[AFR][1000 genomes]
rs229961	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs229963	1.00[AFR][1000 genomes]
rs229965	1.00[AFR][1000 genomes]
rs230846	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs230853	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs230860	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs230861	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2408846	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408847	1.00[ASN][1000 genomes]
rs2408850	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2408854	0.87[MKK][hapmap];1.00[YRI][hapmap]
rs2568537	1.00[YRI][hapmap]
rs2898028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4141129	1.00[ASN][1000 genomes]
rs4235474	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4285175	0.87[MKK][hapmap]
rs4403130	0.87[MKK][hapmap];1.00[YRI][hapmap]
rs4458541	0.87[MKK][hapmap];1.00[YRI][hapmap]
rs4508990	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4588536	0.82[EUR][1000 genomes]
rs4699910	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4699913	0.87[MKK][hapmap];1.00[YRI][hapmap]
rs4700214	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4700217	1.00[ASN][1000 genomes]
rs4700233	0.87[MKK][hapmap];1.00[YRI][hapmap]
rs6450430	0.86[EUR][1000 genomes]
rs6450431	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6866242	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6875712	0.82[EUR][1000 genomes]
rs6879952	0.81[EUR][1000 genomes]
rs6886241	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7726732	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7732108	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7737409	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs854036	1.00[YRI][hapmap]
rs917655	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9292141	1.00[ASN][1000 genomes]
rs986101	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs991727	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[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	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
3	nsv830310	chr5:56989346-57176006	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
4	esv2763454	chr5:57006531-57161140	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2408849	CDC20B	cis	cerebellum	SCAN
rs2408849	TADA2B	trans	parietal	SCAN
rs2408849	GZMK	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57021800-57030400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:57028600-57030000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:57028600-57031200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr5:57029000-57029400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:57029000-57030000	Weak transcription	Fetal Lung	lung
6	chr5:57029000-57034600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:57029200-57029400	Enhancers	Aorta	Aorta

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