Variant report

Variant	rs7035117
Chromosome Location	chr9:94684351-94684352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94682144..94685075-chr9:94711793..94713631,2	MCF-7	breast:
2	chr9:94664745..94669992-chr9:94681267..94685780,5	K562	blood:
3	chr9:94667170..94669992-chr9:94682219..94685194,2	K562	blood:

Variant related genes	Relation type
ENSG00000169071	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10046835	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10114686	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10115262	0.89[CHB][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10118781	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119983	1.00[CEU][hapmap]
rs10120655	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10122619	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124796	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512218	1.00[CEU][hapmap]
rs10512219	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10992160	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992163	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992175	0.81[EUR][1000 genomes]
rs12340061	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12341791	1.00[CEU][hapmap]
rs12344469	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12349258	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16907940	1.00[CEU][hapmap]
rs1919104	1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58964193	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59195968	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59917975	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60351369	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61266489	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027147	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7036958	0.86[ASN][1000 genomes]
rs7043019	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7045073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7045602	0.88[GIH][hapmap]
rs7045603	0.86[ASN][1000 genomes]
rs73519176	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73520858	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73520881	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73520889	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7856148	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7863425	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7875037	0.89[CHB][hapmap];1.00[JPT][hapmap]

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
rs7035117	SPTLC1	cis	multi-tissue	Pritchard

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94670600-94686200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:94678000-94685000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr9:94678200-94686600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:94678800-94686200	Weak transcription	Ovary	ovary
5	chr9:94681400-94691400	Weak transcription	Pancreas	Pancrea
6	chr9:94682600-94684600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr9:94683000-94684600	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr9:94683000-94684600	Enhancers	Stomach Smooth Muscle	stomach
9	chr9:94683000-94687200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr9:94683400-94686200	Weak transcription	Gastric	stomach
11	chr9:94683600-94684400	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:94683600-94684600	Weak transcription	Right Atrium	heart
13	chr9:94683600-94685200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:94683600-94685200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr9:94683600-94685200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr9:94683600-94686000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:94683600-94691800	Weak transcription	Fetal Lung	lung
18	chr9:94683600-94692000	Weak transcription	K562	blood
19	chr9:94683800-94685800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr9:94683800-94685800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr9:94684000-94684400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:94684000-94684800	Weak transcription	Fetal Stomach	stomach
23	chr9:94684000-94686000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:94684200-94686600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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