Variant report

Variant	rs1865531
Chromosome Location	chr4:147096093-147096094
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	chr4:147086830..147091007-chr4:147091903..147096779,4	K562	blood:
2	chr4:147095588..147099041-chr4:147101501..147104102,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164167	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10000407	0.80[AMR][1000 genomes]
rs10017509	0.84[CEU][hapmap]
rs10021707	0.87[YRI][hapmap]
rs10519776	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1079476	0.98[ASN][1000 genomes]
rs11100919	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721367	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721873	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722991	0.84[CEU][hapmap]
rs11723069	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11724307	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11728525	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11728609	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729787	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11730306	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11733347	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734320	0.84[CEU][hapmap]
rs11940961	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs12152657	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152692	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152709	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12186313	0.81[CEU][hapmap]
rs17021106	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17021186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021217	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021239	0.82[CEU][hapmap]
rs17021241	0.91[CEU][hapmap]
rs17756234	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17757522	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757685	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757715	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17758092	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17758396	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17758420	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814023	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814065	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814503	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814598	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864371	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1865532	0.82[EUR][1000 genomes]
rs2007366	0.80[AMR][1000 genomes]
rs2068009	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115796	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115797	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163171	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164280	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28420466	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733458	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733459	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733460	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3733461	0.84[CEU][hapmap]
rs3756081	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756082	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4282199	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835283	0.81[CEU][hapmap]
rs4835284	0.84[CEU][hapmap]
rs4835286	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs55736910	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56174047	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56279747	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56333123	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56393662	0.98[ASN][1000 genomes]
rs62326797	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62326801	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62326802	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62326804	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326848	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537400	0.80[AMR][1000 genomes]
rs6537401	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537402	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537403	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813969	0.82[CEU][hapmap]
rs6815527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816161	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821066	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821444	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821479	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821863	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824313	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838174	0.84[CEU][hapmap]
rs6838458	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6839123	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839141	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843421	0.82[CEU][hapmap]
rs6844381	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856647	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6858813	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72727944	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72727952	0.98[ASN][1000 genomes]
rs7657269	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665079	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695415	0.80[AMR][1000 genomes]
rs7745	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919483	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv1018859	chr4:147055618-147138397	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1865531	RP11-6L6.2	cis	Esophagus Muscularis	GTEx
rs1865531	RP11-6L6.2	cis	Thyroid	GTEx
rs1865531	RP11-6L6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs1865531	RP11-6L6.2	cis	Nerve Tibial	GTEx
rs1865531	RP11-6L6.2	cis	Adipose Subcutaneous	GTEx
rs1865531	RP11-6L6.2	cis	lung	GTEx
rs1865531	RP11-6L6.2	cis	Whole Blood	GTEx
rs1865531	RP11-6L6.2	cis	Artery Tibial	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147095200-147096200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr4:147095200-147096600	Weak transcription	Ovary	ovary
3	chr4:147095400-147096400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr4:147095400-147096400	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr4:147096000-147096200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:147096000-147096200	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr4:147096000-147096200	Enhancers	Brain Hippocampus Middle	brain
8	chr4:147096000-147096200	Enhancers	Dnd41	blood
9	chr4:147096000-147096400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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