Variant report

Variant	rs60351369
Chromosome Location	chr9:94680289-94680290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94676298..94678105-chr9:94680028..94681662,2	MCF-7	breast:
2	chr9:94668680..94671587-chr9:94678743..94680656,2	K562	blood:
3	chr9:94680096..94683212-chr9:94691490..94694919,3	K562	blood:
4	chr9:94679676..94683212-chr9:94692527..94694919,4	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10046835	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10114686	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10115262	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10118781	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10120655	0.86[ASN][1000 genomes]
rs10122619	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10124796	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992160	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992163	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992175	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12340061	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12344469	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12349258	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919104	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58964193	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59195968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59917975	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61266489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027147	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7035117	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036958	0.86[ASN][1000 genomes]
rs7043019	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7045073	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7045603	0.86[ASN][1000 genomes]
rs73519176	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73520858	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73520881	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73520889	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7856148	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7863425	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][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
rs60351369	SPTLC1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94668800-94682800	Weak transcription	Colonic Mucosa	Colon
2	chr9:94670200-94682800	Weak transcription	Fetal Kidney	kidney
3	chr9:94670400-94681200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:94670400-94682800	Weak transcription	Right Atrium	heart
5	chr9:94670600-94686200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:94671600-94682600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:94677400-94683000	Weak transcription	K562	blood
8	chr9:94677600-94682800	Weak transcription	Fetal Intestine Large	intestine
9	chr9:94678000-94685000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:94678200-94683600	Enhancers	Colon Smooth Muscle	Colon
11	chr9:94678200-94686600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:94678800-94686200	Weak transcription	Ovary	ovary
13	chr9:94679200-94680800	Weak transcription	Fetal Lung	lung
14	chr9:94679600-94681400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:94679600-94682800	Weak transcription	Fetal Heart	heart
16	chr9:94679600-94684200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:94679800-94681000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr9:94679800-94681200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr9:94680000-94681200	Enhancers	Stomach Smooth Muscle	stomach
20	chr9:94680000-94682000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:94680000-94682000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:94680200-94682600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr9:94680200-94682800	Weak transcription	Fetal Stomach	stomach

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