Variant report

Variant	rs1565717
Chromosome Location	chr1:76320441-76320442
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:76262942..76264627-chr1:76319779..76321493,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10732723	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs10782558	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873788	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs10873808	0.80[AMR][1000 genomes]
rs11161510	0.84[GIH][hapmap]
rs11161521	0.84[GIH][hapmap]
rs11161620	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161626	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161792	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11161836	0.87[CEU][hapmap]
rs11161845	0.80[AMR][1000 genomes]
rs11161857	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs1144336	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146581	0.81[GIH][hapmap]
rs1146646	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146653	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588578	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs1159214	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap]
rs12021855	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12090849	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap]
rs12093623	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118399	0.80[AMR][1000 genomes]
rs12122939	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127078	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136360	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568447	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12723575	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17650138	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs1770885	0.90[CEU][hapmap]
rs1770887	0.87[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap]
rs2029681	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2029683	0.87[CEU][hapmap];1.00[CHB][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2172507	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2172508	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2347962	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2881786	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4949677	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949686	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs4949885	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745336	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745363	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745381	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5745390	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5745427	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5745433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5745442	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs5745449	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs61770533	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61770550	0.80[AMR][1000 genomes]
rs6678348	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6683437	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs6699682	0.93[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.99[MKK][hapmap];0.91[TSI][hapmap]
rs7523573	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs7538800	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7547056	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549863	1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs931507	0.87[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1795237	chr1:76268573-76383565	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1800125	chr1:76269439-76379497	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1799260	chr1:76269439-76383297	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv1847721	chr1:76269439-76383565	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1004669	chr1:76301198-76409451	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv871671	chr1:76304215-76391646	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1565717	MSH4	cis	Artery Tibial	GTEx
rs1565717	SNORD45B	cis	parietal	SCAN
rs1565717	ACADM	cis	cerebellum	SCAN
rs1565717	MSH4	cis	parietal	SCAN
rs1565717	MSH4	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76319600-76327400	Weak transcription	Aorta	Aorta
2	chr1:76320000-76320800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:76320000-76321400	Enhancers	HepG2	liver
4	chr1:76320000-76321400	Enhancers	K562	blood
5	chr1:76320400-76321000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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