Variant report

Variant	rs10992158
Chromosome Location	chr9:94674927-94674928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94666595..94672238-chr9:94672403..94678372,8	K562	blood:
2	chr9:94673282..94676556-chr9:94680783..94682805,3	K562	blood:
3	chr9:94673439..94675902-chr9:94676796..94680111,3	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10761137	0.82[EUR][1000 genomes]
rs10820914	0.83[CEU][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10820915	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992149	0.86[JPT][hapmap];0.82[AMR][1000 genomes]
rs10992151	0.83[CEU][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10992159	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10992161	0.96[TSI][hapmap]
rs11789973	0.83[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11792319	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12683797	0.84[GIH][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs1609292	0.84[EUR][1000 genomes]
rs1881384	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1892263	0.96[TSI][hapmap]
rs1919102	0.81[EUR][1000 genomes]
rs1919103	0.85[EUR][1000 genomes]
rs2030992	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3905385	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4275276	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4347043	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4347044	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4430151	0.87[CEU][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4517189	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4744113	0.80[JPT][hapmap]
rs57688942	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58431919	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59723153	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62565678	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62565679	0.82[EUR][1000 genomes]
rs62565747	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6479383	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs72746246	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv530946	chr9:94633154-94715023	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10992158	SPTLC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94668800-94676800	Weak transcription	Fetal Intestine Large	intestine
2	chr9:94668800-94676800	Weak transcription	Spleen	Spleen
3	chr9:94668800-94682800	Weak transcription	Colonic Mucosa	Colon
4	chr9:94669200-94676600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr9:94670200-94678000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr9:94670200-94678400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:94670200-94682800	Weak transcription	Fetal Kidney	kidney
8	chr9:94670400-94681200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:94670400-94682800	Weak transcription	Right Atrium	heart
10	chr9:94670600-94676400	Weak transcription	Fetal Muscle Leg	muscle
11	chr9:94670600-94686200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:94670800-94676400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:94671600-94676800	Weak transcription	Fetal Intestine Small	intestine
14	chr9:94671600-94676800	Weak transcription	Fetal Stomach	stomach
15	chr9:94671600-94682600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:94671800-94676400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:94671800-94677000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:94671800-94678200	Weak transcription	Fetal Lung	lung
19	chr9:94671800-94678200	Weak transcription	Ovary	ovary
20	chr9:94673600-94675200	Weak transcription	Esophagus	oesophagus
21	chr9:94674200-94675600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:94674400-94675800	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:94674400-94676600	Weak transcription	K562	blood
24	chr9:94674600-94677400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:94674600-94679400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr9:94674600-94679400	Weak transcription	Rectal Smooth Muscle	rectum

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