Variant report

Variant	rs11789730
Chromosome Location	chr9:94631730-94631731
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	chr9:94626758..94629803-chr9:94629808..94631771,3	K562	blood:
2	chr9:94631306..94632967-chr9:94636056..94637975,2	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10820905	0.80[EUR][1000 genomes]
rs10820906	0.81[CEU][hapmap]
rs10992123	0.92[CEU][hapmap]
rs10992124	0.87[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes]
rs10992126	0.83[EUR][1000 genomes]
rs10992128	0.88[CEU][hapmap]
rs10992129	0.85[CEU][hapmap]
rs10992130	0.83[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap]
rs10992132	0.87[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap]
rs10992134	0.87[CEU][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs10992135	0.83[CEU][hapmap]
rs10992136	0.96[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10992137	0.87[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap]
rs10992139	0.87[CEU][hapmap]
rs10992142	0.92[CEU][hapmap]
rs10992143	0.91[CEU][hapmap]
rs10992144	0.92[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs10992145	0.96[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs11790144	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11791450	0.81[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs12376130	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12378938	0.89[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs12551140	0.87[CEU][hapmap]
rs12552292	0.85[CEU][hapmap]
rs12552858	0.95[CEU][hapmap]
rs12555334	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12684524	0.83[CEU][hapmap];0.83[MEX][hapmap]
rs1528363	0.83[CEU][hapmap]
rs1528364	0.83[CEU][hapmap]
rs1534530	0.84[EUR][1000 genomes]
rs16907887	0.88[CEU][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap]
rs1881385	0.92[CEU][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.83[EUR][1000 genomes]
rs1881387	0.92[CEU][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap];0.80[AMR][1000 genomes]
rs1881392	0.87[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap]
rs2030991	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2312732	0.83[CEU][hapmap]
rs2312733	0.82[EUR][1000 genomes]
rs2312734	0.87[CEU][hapmap]
rs2312735	0.92[CEU][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.84[EUR][1000 genomes]
rs4322068	0.82[CEU][hapmap]
rs4639579	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs4743857	0.83[CEU][hapmap]
rs4744107	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs55663665	0.81[AMR][1000 genomes]
rs55956910	0.84[EUR][1000 genomes]
rs56308784	0.80[AMR][1000 genomes]
rs58202197	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6479374	0.83[CEU][hapmap]
rs6479375	0.83[CEU][hapmap]
rs6479376	0.88[CEU][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap]
rs67944481	0.80[AMR][1000 genomes]
rs7029950	0.83[CEU][hapmap]
rs7030661	0.96[CEU][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7031562	0.83[CEU][hapmap]
rs7033819	0.92[CEU][hapmap]
rs7039406	0.87[CEU][hapmap]
rs7045226	0.96[CEU][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7048756	0.83[CEU][hapmap]
rs7847473	0.84[EUR][1000 genomes]
rs7850118	0.92[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7855417	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs7856144	0.83[CEU][hapmap]
rs7859331	0.83[CEU][hapmap]
rs7863061	0.87[CEU][hapmap]
rs7864311	0.84[EUR][1000 genomes]
rs7865855	0.84[EUR][1000 genomes]
rs7867707	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs7870902	0.81[AMR][1000 genomes]
rs7874148	0.83[CEU][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11789730	SPTLC1	cis	parietal	SCAN
rs11789730	BET1	trans	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94621400-94638000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:94623200-94634000	Weak transcription	Fetal Intestine Small	intestine
3	chr9:94626600-94636200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:94627000-94632600	Weak transcription	Right Atrium	heart
5	chr9:94627000-94635000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:94627000-94650800	Weak transcription	Gastric	stomach
7	chr9:94627200-94648600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr9:94627600-94647400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:94628000-94635400	Weak transcription	Fetal Heart	heart
10	chr9:94628400-94632400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr9:94629800-94633800	Weak transcription	Fetal Stomach	stomach
12	chr9:94630200-94634600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:94630200-94636200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr9:94630200-94636400	Weak transcription	Ovary	ovary
15	chr9:94630400-94632800	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:94630400-94633400	Weak transcription	Fetal Lung	lung
17	chr9:94630400-94641400	Weak transcription	K562	blood
18	chr9:94631200-94639400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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