Variant report

Variant	rs4869324
Chromosome Location	chr5:96567390-96567391
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10044182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10070105	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1018058	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10476561	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10476701	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10515256	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11746308	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11746330	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13162261	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13171520	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13178119	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1423501	1.00[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1423502	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1423503	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1423504	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1423507	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1528593	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1528598	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1528599	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1581662	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17630601	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17630655	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1845649	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1845652	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1862593	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1874292	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1919246	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2081143	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2088150	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2222767	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2463784	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2548419	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2548421	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2548426	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2548427	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2643487	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2643490	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2643491	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2643492	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2643493	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2643494	0.81[EUR][1000 genomes]
rs2643495	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2643497	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2643498	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2643500	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2643531	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2643532	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2643567	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2697569	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2697570	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2697575	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2697576	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2697577	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2697578	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2697579	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2697580	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2697581	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2697582	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2697599	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2697600	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2697601	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2697602	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2697603	0.84[EUR][1000 genomes]
rs2697604	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2697605	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2697606	0.84[EUR][1000 genomes]
rs2697611	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2697644	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28808625	0.81[AFR][1000 genomes]
rs3108531	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3108532	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34089335	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34122360	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35498938	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36154380	0.83[EUR][1000 genomes]
rs4032064	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4073423	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4242236	0.89[CEU][hapmap]
rs4869151	0.85[CHB][hapmap];0.80[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap]
rs4869154	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4869155	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56267018	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67340817	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6861811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs721801	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72777631	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72777640	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72777653	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7449164	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7729001	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9314195	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS 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	66 gene(s)	inside rSNPs	diseases
2	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv830412	chr5:96427305-96606619	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1019790	chr5:96471680-96980633	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv537812	chr5:96471680-96980633	ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv882393	chr5:96496189-96567950	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv534326	chr5:96531217-97283481	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv882394	chr5:96538585-97108559	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1032548	chr5:96565121-97046804	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv537813	chr5:96565121-97046804	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4869324	MCTP1	cis	parietal	SCAN
rs4869324	PARP8	trans	parietal	SCAN
rs4869324	ARSK	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96565600-96571200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:96566800-96567400	Enhancers	Dnd41	blood
3	chr5:96567000-96567400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:96567000-96567400	Enhancers	Brain Hippocampus Middle	brain
5	chr5:96567000-96567400	Enhancers	Brain Substantia Nigra	brain

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