Variant report

Variant	rs10992124
Chromosome Location	chr9:94584452-94584453
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:94580430..94582585-chr9:94584118..94590050,5	K562	blood:
2	chr9:94580430..94582759-chr9:94584118..94590023,5	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10820906	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs10820907	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10820908	0.85[EUR][1000 genomes]
rs10820910	0.84[CEU][hapmap]
rs10992123	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992128	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10992129	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992130	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992131	0.91[CEU][hapmap]
rs10992132	0.91[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992134	0.84[CEU][hapmap]
rs10992135	0.87[CEU][hapmap]
rs10992136	0.83[CEU][hapmap]
rs10992137	0.91[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992139	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992140	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10992143	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10992145	0.88[CEU][hapmap]
rs11789730	0.87[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes]
rs11789973	0.82[TSI][hapmap]
rs11790144	0.83[CEU][hapmap]
rs11791450	0.91[CEU][hapmap]
rs12376130	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs12376231	0.81[EUR][1000 genomes]
rs12376539	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs12378938	0.89[CEU][hapmap]
rs12551140	0.92[CEU][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12552292	0.85[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12552858	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12555334	0.81[CEU][hapmap]
rs12683797	0.80[CHB][hapmap]
rs12684524	0.87[CEU][hapmap];0.80[MEX][hapmap]
rs1528363	0.87[CEU][hapmap]
rs1528364	0.87[CEU][hapmap]
rs1534531	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1534533	0.84[CEU][hapmap]
rs16907887	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1881385	0.87[CEU][hapmap]
rs1881387	0.87[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1881392	0.91[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1997286	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2141368	0.91[TSI][hapmap]
rs2312732	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2312734	0.92[CEU][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2312735	0.87[CEU][hapmap]
rs2841691	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4322068	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs4639579	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743857	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs4744108	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4744109	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs4744110	0.93[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs4744111	0.84[CEU][hapmap]
rs4744113	0.80[CHB][hapmap]
rs55663665	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55864279	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56088447	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56308784	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62564595	0.81[EUR][1000 genomes]
rs62564597	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62564599	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62565674	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6479374	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs6479375	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs6479376	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67944481	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7019210	0.81[EUR][1000 genomes]
rs7029950	0.87[CEU][hapmap]
rs7030661	0.84[CEU][hapmap]
rs7031562	0.87[CEU][hapmap]
rs7033819	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7039406	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7045226	0.84[CEU][hapmap]
rs7045333	0.82[EUR][1000 genomes]
rs7048756	0.87[CEU][hapmap]
rs72746206	0.82[EUR][1000 genomes]
rs7850118	0.88[CEU][hapmap]
rs7850636	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7855417	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7856144	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs7859331	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs7863061	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7867707	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7870049	0.80[CEU][hapmap]
rs7870902	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7874148	0.87[CEU][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045332	chr9:94352661-94656016	Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv531631	chr9:94373847-94633213	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1036176	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv540171	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv518372	chr9:94558126-94605908	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv6614	chr9:94571349-94610085	ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10992124	SPTLC1	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94572400-94587400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr9:94576800-94586200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:94580000-94585000	Weak transcription	Esophagus	oesophagus
4	chr9:94581000-94586400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr9:94581800-94586600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:94581800-94587600	Weak transcription	Spleen	Spleen
7	chr9:94581800-94588000	Weak transcription	Fetal Kidney	kidney
8	chr9:94582400-94586200	Weak transcription	Fetal Lung	lung
9	chr9:94583800-94584800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:94583800-94585200	ZNF genes & repeats	Fetal Stomach	stomach
11	chr9:94583800-94586200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:94583800-94586400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr9:94583800-94586800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr9:94584000-94585400	Weak transcription	Ovary	ovary
15	chr9:94584000-94587200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:94584000-94595800	Weak transcription	Gastric	stomach
17	chr9:94584200-94586000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:94584200-94586000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr9:94584200-94586200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr9:94584200-94586400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr9:94584200-94587400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr9:94584400-94585200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:94584400-94586400	Weak transcription	Colon Smooth Muscle	Colon

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