Variant report

Variant	rs1933679
Chromosome Location	chr9:96709022-96709023
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10117457	0.87[EUR][1000 genomes]
rs10122334	0.83[CEU][hapmap]
rs10123954	0.88[EUR][1000 genomes]
rs10429556	0.89[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs10429603	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10435922	0.89[EUR][1000 genomes]
rs10435924	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10739967	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10739969	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.88[MEX][hapmap]
rs10761308	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10761309	0.86[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10761313	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10761315	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.82[MEX][hapmap]
rs10821284	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10821285	0.93[CEU][hapmap];0.85[CHB][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10993037	0.83[EUR][1000 genomes]
rs10993058	0.81[CEU][hapmap]
rs12351292	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12684427	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1316814	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1320547	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1331216	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1331217	0.93[CEU][hapmap];0.85[CHB][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1331218	0.92[CEU][hapmap];0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1331219	0.96[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1343995	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1360429	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1411860	0.93[CEU][hapmap];0.85[CHB][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1418251	0.89[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs1576640	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1590969	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1592153	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1832857	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1854835	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1933667	0.81[EUR][1000 genomes]
rs1933668	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1933669	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2026917	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2094927	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2150625	0.89[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2153058	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2153070	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2153792	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2211362	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2225458	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2226117	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3847307	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap]
rs3996241	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4282631	0.96[CEU][hapmap];0.85[CHB][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4744308	0.89[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes]
rs4744310	0.87[EUR][1000 genomes]
rs4744316	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.88[MEX][hapmap]
rs6479522	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6479527	0.81[CEU][hapmap];0.81[GIH][hapmap]
rs6479528	0.81[CEU][hapmap];0.81[GIH][hapmap]
rs7033481	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7033898	0.93[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7045643	0.89[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs7858069	0.93[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7867253	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7867925	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs914295	0.89[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs914296	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs914297	0.89[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes]
rs9299414	0.88[CEU][hapmap];0.88[CHB][hapmap];0.88[EUR][1000 genomes]
rs987511	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1035418	chr9:96647940-96711409	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv824993	chr9:96699362-96725105	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv893590	chr9:96701287-96729129	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1933679	ORMDL2	trans	parietal	SCAN
rs1933679	SPTLC1	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96708400-96709200	Enhancers	Pancreas	Pancrea
2	chr9:96708600-96709200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:96708600-96709200	Bivalent Enhancer	Fetal Stomach	stomach
4	chr9:96708600-96709200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
5	chr9:96708600-96710600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:96708600-96713000	Weak transcription	Gastric	stomach
7	chr9:96708800-96709200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
8	chr9:96708800-96709200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:96708800-96710000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
10	chr9:96708800-96710400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
11	chr9:96708800-96710400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
12	chr9:96709000-96709200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr9:96709000-96709600	Enhancers	Stomach Smooth Muscle	stomach
14	chr9:96709000-96713200	Weak transcription	Right Atrium	heart

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