Variant report

Variant	rs724248
Chromosome Location	chr9:93209923-93209924
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10465157	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10465158	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10465163	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10512198	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10761365	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10761367	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10761373	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10821416	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10821417	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10821418	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10821419	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10821420	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10821421	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10821422	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10821423	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10821424	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10821425	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10821426	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10821427	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10821429	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10821434	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10821435	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10821443	0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[MEX][hapmap];0.80[MKK][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10821444	1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[MEX][hapmap];0.80[MKK][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10821445	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10821448	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10821452	0.80[JPT][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10993461	0.83[ASN][1000 genomes]
rs10993468	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10993469	1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10993470	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12377373	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1529333	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1930923	0.81[JPT][hapmap];0.88[EUR][1000 genomes]
rs2114350	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs2217094	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2217095	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386532	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2892055	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3748185	0.87[CHB][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3748186	0.87[CHB][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3748187	0.87[CHB][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4237223	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4237224	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4595251	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4743985	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4743986	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4743987	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4744413	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4744414	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4744415	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4744416	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4744417	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4744418	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4744439	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6479595	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7029610	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7030038	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046597	0.84[CEU][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs7047032	0.84[CEU][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes]
rs7869492	0.83[AMR][1000 genomes]
rs7870764	1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs883922	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs913619	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs913620	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs913621	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs913622	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9332454	0.87[CHB][hapmap];0.90[CHD][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs944901	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs944902	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs944903	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs944904	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041278	chr9:92965701-93560454	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv482748	chr9:93123377-93279526	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv893565	chr9:93130796-93392332	Genic enhancers Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv614853	chr9:93183404-93266508	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv614854	chr9:93209923-93266508	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv893566	chr9:93209923-93439259	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs724248	SPTLC1	cis	parietal	SCAN
rs724248	GOLM1	cis	cerebellum	SCAN
rs724248	LOC440173	cis	cerebellum	SCAN
rs724248	RP11-389K14.3	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93196200-93220800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:93204600-93210200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:93206000-93211400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:93206400-93222600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:93207800-93213800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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