Variant report

Variant	rs10000407
Chromosome Location	chr4:147055307-147055308
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10017509	0.88[CEU][hapmap]
rs10519776	0.83[EUR][1000 genomes]
rs11100919	0.83[EUR][1000 genomes]
rs11721873	0.83[EUR][1000 genomes]
rs11722991	0.88[CEU][hapmap]
rs11723069	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11724307	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725678	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11728525	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728609	0.83[EUR][1000 genomes]
rs11729787	0.83[EUR][1000 genomes]
rs11730306	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11733347	0.83[EUR][1000 genomes]
rs11734320	0.88[CEU][hapmap]
rs11940961	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12152657	0.83[EUR][1000 genomes]
rs12152709	0.83[EUR][1000 genomes]
rs12186313	0.88[CEU][hapmap]
rs17021106	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17021186	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs17021217	0.83[EUR][1000 genomes]
rs17021239	0.82[CEU][hapmap]
rs17021241	0.83[CEU][hapmap]
rs17756056	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17756234	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17757522	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs17757685	0.92[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes]
rs17757715	0.83[EUR][1000 genomes]
rs17758092	0.83[EUR][1000 genomes]
rs17758396	0.82[EUR][1000 genomes]
rs17758420	0.83[EUR][1000 genomes]
rs17814023	0.83[EUR][1000 genomes]
rs17814065	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs17814503	0.83[EUR][1000 genomes]
rs17814598	0.83[EUR][1000 genomes]
rs1812385	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1864371	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1865531	0.92[CEU][hapmap];0.85[CHB][hapmap];0.80[AMR][1000 genomes]
rs2007366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068009	0.83[EUR][1000 genomes]
rs2115796	0.83[EUR][1000 genomes]
rs2115797	0.83[EUR][1000 genomes]
rs2163171	0.83[EUR][1000 genomes]
rs28393640	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3733461	0.88[CEU][hapmap]
rs3756081	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs3756082	0.83[EUR][1000 genomes]
rs3756083	0.80[AMR][1000 genomes]
rs3775498	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs3815967	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs3948408	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4549398	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835283	0.88[CEU][hapmap]
rs4835284	0.88[CEU][hapmap]
rs4835286	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55736910	0.83[EUR][1000 genomes]
rs56174047	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56279747	0.83[EUR][1000 genomes]
rs56289966	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56333123	0.83[EUR][1000 genomes]
rs62326764	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326797	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62326804	0.83[EUR][1000 genomes]
rs62326848	0.83[EUR][1000 genomes]
rs6537399	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537400	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813969	0.82[CEU][hapmap]
rs6815527	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs6816161	0.92[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes]
rs6820462	0.92[CEU][hapmap];0.85[CHB][hapmap]
rs6821066	0.83[EUR][1000 genomes]
rs6821479	0.83[EUR][1000 genomes]
rs6824313	0.83[EUR][1000 genomes]
rs6832576	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838174	0.85[CEU][hapmap]
rs6838458	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6839123	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs6839141	0.83[EUR][1000 genomes]
rs6843421	0.82[CEU][hapmap]
rs6844381	0.83[EUR][1000 genomes]
rs6856647	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72727922	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7657269	0.84[EUR][1000 genomes]
rs7695415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745	0.83[EUR][1000 genomes]
rs919482	0.92[CEU][hapmap];0.85[CHB][hapmap]
rs919483	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs9308199	0.96[CEU][hapmap];0.82[CHB][hapmap]

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	nsv461674	chr4:147047072-147143572	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv595650	chr4:147047072-147143572	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10000407	RP11-6L6.2	cis	Nerve Tibial	GTEx
rs10000407	RP11-6L6.2	cis	Artery Tibial	GTEx
rs10000407	RP11-6L6.2	cis	Adipose Subcutaneous	GTEx
rs10000407	RP11-6L6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10000407	RP11-6L6.2	cis	lung	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147045800-147055400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:147052600-147056000	Weak transcription	Right Atrium	heart
3	chr4:147054000-147055600	Weak transcription	Esophagus	oesophagus
4	chr4:147054600-147055800	Weak transcription	Osteobl	bone
5	chr4:147054600-147056600	Enhancers	Fetal Brain Male	brain
6	chr4:147055200-147056600	Enhancers	Fetal Brain Female	brain
7	chr4:147055200-147057400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr4:147055200-147057400	Enhancers	Cortex derived primary cultured neurospheres	brain

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