Variant report

Variant	rs10761309
Chromosome Location	chr9:96753722-96753723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:112089787..112092208-chr9:96752940..96755757,2	MCF-7	breast:
2	chr9:96747770..96750246-chr9:96753383..96755381,2	K562	blood:

Variant related genes	Relation type
ENSG00000006652	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10117457	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10122334	0.87[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10123954	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10429556	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10429603	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10435922	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10435924	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10739967	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739969	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10761308	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761313	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10761315	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs10821284	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821285	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10993010	0.85[AFR][1000 genomes]
rs10993037	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10993041	0.82[EUR][1000 genomes]
rs10993058	0.84[CEU][hapmap]
rs12351292	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12684427	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1316814	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320547	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1331216	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1331217	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1331218	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1331219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1343995	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1360429	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411860	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418251	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1576640	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1590969	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1592153	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1832857	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1854835	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1933667	0.80[EUR][1000 genomes]
rs1933668	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1933669	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1933679	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2026917	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2094927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150625	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2153058	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2153070	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2153792	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211362	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2225458	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2226117	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35883789	0.80[EUR][1000 genomes]
rs3847307	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.82[ASN][1000 genomes]
rs3996241	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4282631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4406469	0.81[EUR][1000 genomes]
rs4744308	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4744310	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4744314	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4744316	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs55763839	0.85[AFR][1000 genomes]
rs6479522	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479527	0.85[CEU][hapmap];0.91[GIH][hapmap];0.81[TSI][hapmap]
rs6479528	0.85[CEU][hapmap];0.91[GIH][hapmap];0.81[TSI][hapmap]
rs7033481	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7033898	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7045643	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7858069	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7867253	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7867925	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs914295	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs914296	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914297	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9299414	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9695457	0.83[AFR][1000 genomes]
rs987511	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10761309	SPTLC1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96742000-96764200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr9:96749000-96756400	Weak transcription	Gastric	stomach
3	chr9:96752400-96753800	ZNF genes & repeats	Liver	Liver
4	chr9:96753000-96756600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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