Variant report

Variant	rs6866242
Chromosome Location	chr5:57041100-57041101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10054371	0.87[EUR][1000 genomes]
rs10057880	1.00[YRI][hapmap]
rs10072292	1.00[YRI][hapmap]
rs10077005	0.86[AFR][1000 genomes]
rs1016457	0.87[EUR][1000 genomes]
rs10213766	0.87[EUR][1000 genomes]
rs1023572	0.87[EUR][1000 genomes]
rs1023573	0.87[EUR][1000 genomes]
rs10487613	0.86[AFR][1000 genomes]
rs10487614	0.86[AFR][1000 genomes]
rs12520986	0.86[AFR][1000 genomes]
rs13185580	0.86[AFR][1000 genomes]
rs1347071	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs170740	0.86[AFR][1000 genomes]
rs1821210	1.00[MKK][hapmap];1.00[YRI][hapmap]
rs183477	0.86[AFR][1000 genomes]
rs1861052	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1861055	0.86[EUR][1000 genomes]
rs1861056	0.87[EUR][1000 genomes]
rs1861059	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2017201	0.86[AFR][1000 genomes]
rs2041678	0.86[AFR][1000 genomes]
rs2191445	0.86[AFR][1000 genomes]
rs2191446	0.86[AFR][1000 genomes]
rs2191448	0.86[AFR][1000 genomes]
rs2215420	0.86[AFR][1000 genomes]
rs229960	0.86[AFR][1000 genomes]
rs229961	0.86[AFR][1000 genomes]
rs229963	0.86[AFR][1000 genomes]
rs229965	0.86[AFR][1000 genomes]
rs230853	0.86[AFR][1000 genomes]
rs230860	0.86[AFR][1000 genomes]
rs230861	0.86[AFR][1000 genomes]
rs2408849	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2408850	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2408854	1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2568537	0.90[CHB][hapmap];1.00[YRI][hapmap]
rs2898028	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4235474	0.86[AFR][1000 genomes]
rs4285175	1.00[MKK][hapmap]
rs4403130	1.00[MKK][hapmap];1.00[YRI][hapmap]
rs4458541	1.00[MKK][hapmap];1.00[YRI][hapmap]
rs4508990	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4588536	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4699910	0.86[AFR][1000 genomes]
rs4699913	1.00[MKK][hapmap];1.00[YRI][hapmap]
rs4700214	0.86[AFR][1000 genomes]
rs4700233	1.00[MKK][hapmap];1.00[YRI][hapmap]
rs6450431	0.86[AFR][1000 genomes]
rs6868969	0.87[EUR][1000 genomes]
rs6875712	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6879952	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6886241	0.86[AFR][1000 genomes]
rs6890613	0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs7708665	0.80[EUR][1000 genomes]
rs7726732	0.86[AFR][1000 genomes]
rs7732108	0.86[AFR][1000 genomes]
rs7735778	0.87[EUR][1000 genomes]
rs854036	0.86[CHB][hapmap];1.00[YRI][hapmap]
rs917655	0.86[AFR][1000 genomes]
rs986101	0.86[AFR][1000 genomes]
rs991727	0.86[AFR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6866242	TADA2B	trans	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57033000-57041400	Weak transcription	NH-A	brain
2	chr5:57033000-57044800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:57033400-57041600	Weak transcription	NHDF-Ad	bronchial
4	chr5:57034200-57042200	Weak transcription	Fetal Kidney	kidney
5	chr5:57037400-57041600	Weak transcription	Osteobl	bone
6	chr5:57037800-57041400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:57037800-57045000	Weak transcription	HMEC	breast
8	chr5:57038600-57042600	Weak transcription	Hela-S3	cervix
9	chr5:57040200-57041800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:57040200-57042600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:57040400-57042400	Enhancers	Brain Germinal Matrix	brain
12	chr5:57040600-57042000	Enhancers	NHLF	lung
13	chr5:57040600-57042600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:57041000-57041600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr5:57041000-57041800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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