Variant report

Variant	rs10429556
Chromosome Location	chr9:96805635-96805636
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	chr9:96804294..96806133-chr9:96926083..96928857,2	K562	blood:
2	chr9:96792256..96795925-chr9:96803341..96805691,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269946	Chromatin interaction
ENSG00000158079	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10117457	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10122334	0.83[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.96[ASN][1000 genomes]
rs10123954	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10429603	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10435922	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10435924	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10739967	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10739969	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.96[ASN][1000 genomes]
rs10761308	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10761309	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]
rs10761313	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10761315	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.94[ASN][1000 genomes]
rs10821284	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10821285	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10821290	0.83[ASN][1000 genomes]
rs10993037	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10993041	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10993058	0.84[CEU][hapmap];0.91[GIH][hapmap]
rs12351292	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12684427	0.89[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1316814	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1320547	0.89[CEU][hapmap];0.95[CHB][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13299545	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1331216	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1331217	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1331218	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1331219	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1343995	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1360429	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1411860	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1418251	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1576640	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1590969	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1592153	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1832857	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1854835	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1933668	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1933669	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1933679	0.85[EUR][1000 genomes]
rs2026917	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2094927	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2150625	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2153058	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2153070	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2153792	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2211362	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2225458	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2226117	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35883789	0.82[EUR][1000 genomes]
rs3847307	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.96[ASN][1000 genomes]
rs3996241	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4282631	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4406469	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4744308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744310	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744314	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744316	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.96[ASN][1000 genomes]
rs6479522	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6479527	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs6479528	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs6479529	0.93[ASN][1000 genomes]
rs7033481	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7033898	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7045643	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7858069	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7867253	0.83[EUR][1000 genomes]
rs7867925	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs914295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914296	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs914297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs987511	0.89[EUR][1000 genomes];0.86[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10429556	ORMDL2	trans	parietal	SCAN
rs10429556	SPTLC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96794200-96828000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:96795400-96823800	Weak transcription	Left Ventricle	heart
3	chr9:96798200-96822400	Weak transcription	Fetal Lung	lung
4	chr9:96800000-96818600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:96805600-96812800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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