Variant report

Variant	rs10992134
Chromosome Location	chr9:94615230-94615231
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94614773..94616690-chr9:94628132..94630664,2	K562	blood:
2	chr9:94602829..94604983-chr9:94613867..94616038,2	K562	blood:
3	chr9:94614773..94617225-chr9:94629164..94630767,2	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10761135	0.82[JPT][hapmap]
rs10820905	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10820906	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10820910	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs10992124	0.84[CEU][hapmap]
rs10992126	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992128	0.84[CEU][hapmap]
rs10992129	0.85[CEU][hapmap]
rs10992130	0.88[CEU][hapmap]
rs10992131	0.92[CEU][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10992132	0.92[CEU][hapmap]
rs10992135	0.96[CEU][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10992136	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992137	0.92[CEU][hapmap]
rs10992139	0.92[CEU][hapmap]
rs10992142	0.96[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes]
rs10992143	0.88[CEU][hapmap]
rs10992144	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10992145	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11789730	0.87[CEU][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs11790144	0.92[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs11791450	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12376130	0.87[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs12376231	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12376539	0.86[CEU][hapmap]
rs12378938	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12551140	0.84[CEU][hapmap];0.80[TSI][hapmap]
rs12552292	0.81[CEU][hapmap]
rs12552858	0.95[CEU][hapmap]
rs12555334	0.81[CEU][hapmap]
rs12684524	0.88[CEU][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes]
rs1528363	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs1528364	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs1534530	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1534533	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs16907887	0.84[CEU][hapmap]
rs1881385	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1881387	0.88[CEU][hapmap]
rs1881392	0.92[CEU][hapmap]
rs2312732	0.88[CEU][hapmap]
rs2312733	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2312734	0.84[CEU][hapmap];0.80[TSI][hapmap]
rs2312735	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4322068	0.87[CEU][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes]
rs4639579	0.84[CEU][hapmap]
rs4743857	0.91[CEU][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4744107	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs4744109	0.83[CEU][hapmap]
rs4744111	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs55956910	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62563412	0.82[EUR][1000 genomes]
rs62564595	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62564598	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6479374	0.88[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6479375	0.88[CEU][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6479376	0.84[CEU][hapmap]
rs7019210	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7029950	0.94[ASW][hapmap];0.88[CEU][hapmap];0.81[GIH][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs7030661	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7031562	0.83[ASW][hapmap];0.96[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7033819	0.88[CEU][hapmap]
rs7039406	0.92[CEU][hapmap]
rs7045226	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7045333	0.80[EUR][1000 genomes]
rs7048756	0.96[CEU][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72746206	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7847473	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7850118	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7855417	0.84[CEU][hapmap]
rs7856144	0.88[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7859331	0.88[CEU][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7863061	0.83[CEU][hapmap]
rs7864311	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865855	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7867707	0.84[CEU][hapmap]
rs7870049	0.97[GIH][hapmap];0.81[JPT][hapmap]
rs7874148	0.88[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10992134	SPTLC1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94601800-94618400	Weak transcription	K562	blood
2	chr9:94606600-94616600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:94606800-94619600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:94607200-94619600	Weak transcription	Fetal Intestine Large	intestine
5	chr9:94607600-94619600	Weak transcription	Fetal Intestine Small	intestine
6	chr9:94608400-94619000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:94609600-94617800	Weak transcription	Colon Smooth Muscle	Colon
8	chr9:94610200-94615400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:94610200-94615600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:94610200-94616400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:94610200-94617400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:94610200-94619000	Weak transcription	Ovary	ovary
13	chr9:94610400-94615400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:94610400-94617400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:94610400-94618600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr9:94610600-94618800	Weak transcription	Fetal Kidney	kidney
17	chr9:94611000-94616600	Weak transcription	Fetal Lung	lung
18	chr9:94611400-94619000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr9:94611600-94616000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:94613000-94615400	Weak transcription	Fetal Stomach	stomach
21	chr9:94615000-94616600	Enhancers	Right Atrium	heart
22	chr9:94615200-94615400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:94615200-94615600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:94615200-94615600	Enhancers	Right Ventricle	heart
25	chr9:94615200-94615800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr9:94615200-94621000	Enhancers	Fetal Heart	heart

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