Variant report

Variant	rs1414403
Chromosome Location	chr1:76627868-76627869
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1032185	0.93[ASN][1000 genomes]
rs10782606	1.00[JPT][hapmap]
rs10873867	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10873869	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11162090	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11162092	1.00[CHB][hapmap]
rs11162095	1.00[CHB][hapmap]
rs11162096	1.00[CHB][hapmap]
rs12048024	1.00[JPT][hapmap]
rs12139215	0.88[EUR][1000 genomes]
rs12140759	0.89[EUR][1000 genomes]
rs1414406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473472	1.00[JPT][hapmap]
rs1486931	1.00[JPT][hapmap]
rs1486933	1.00[JPT][hapmap]
rs1591472	1.00[CHB][hapmap]
rs17098221	0.81[ASN][1000 genomes]
rs17098239	0.81[ASN][1000 genomes]
rs17098252	0.85[ASN][1000 genomes]
rs17098360	0.83[ASN][1000 genomes]
rs1970226	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1999734	0.82[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2631778	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs2783657	0.85[ASN][1000 genomes]
rs289682	0.82[CEU][hapmap]
rs289683	0.83[CEU][hapmap]
rs2992502	0.83[CEU][hapmap]
rs3011987	0.88[EUR][1000 genomes]
rs3011989	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs3011990	1.00[JPT][hapmap]
rs3011997	1.00[CEU][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs366497	0.93[EUR][1000 genomes]
rs370016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs370808	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs370908	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs371955	0.90[EUR][1000 genomes]
rs387214	1.00[CEU][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs389899	0.83[CEU][hapmap]
rs393933	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs398826	0.93[EUR][1000 genomes]
rs402394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs409312	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs409979	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs411398	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs413350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418644	0.83[CEU][hapmap]
rs423152	0.87[CEU][hapmap]
rs425110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs427172	0.90[EUR][1000 genomes]
rs429265	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs430875	0.87[EUR][1000 genomes]
rs431752	0.89[EUR][1000 genomes]
rs434633	0.87[EUR][1000 genomes]
rs438166	0.81[CEU][hapmap]
rs442486	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs448003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs450133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs450636	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs450708	0.83[EUR][1000 genomes]
rs473380	1.00[JPT][hapmap]
rs475686	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs479650	1.00[JPT][hapmap]
rs4949696	1.00[CHB][hapmap]
rs4949697	1.00[CHB][hapmap]
rs517036	0.81[TSI][hapmap]
rs519797	0.89[JPT][hapmap]
rs531773	0.89[JPT][hapmap]
rs532583	0.93[EUR][1000 genomes]
rs533097	0.89[JPT][hapmap]
rs536913	0.89[JPT][hapmap]
rs544010	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs560520	0.86[JPT][hapmap]
rs569850	0.89[JPT][hapmap]
rs572623	0.89[JPT][hapmap]
rs573657	0.89[JPT][hapmap]
rs580928	0.89[JPT][hapmap]
rs603022	1.00[CEU][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs638593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681280	0.80[CEU][hapmap]
rs7556363	1.00[CHB][hapmap]
rs860154	0.83[CEU][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	nsv1488	chr1:76587622-76632635	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv870621	chr1:76620313-76997071	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1414403	KDM5D	trans	lymphoblastoid	seeQTL
rs1414403	XIST	trans	lymphoblastoid	seeQTL
rs1414403	DDX3Y	trans	lymphoblastoid	seeQTL
rs1414403	RPS4Y1	trans	lymphoblastoid	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76619800-76646400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:76621000-76630600	Weak transcription	Psoas Muscle	Psoas
3	chr1:76621000-76630800	Weak transcription	Primary B cells from cord blood	blood
4	chr1:76627600-76628400	Enhancers	Fetal Lung	lung
5	chr1:76627800-76628000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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