Variant report

Variant	rs10115262
Chromosome Location	chr9:94702266-94702267
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	chr9:94700947..94708226-chr9:94708551..94712716,11	K562	blood:

Variant related genes	Relation type
ENSG00000169071	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10046835	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10114686	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10118781	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10120655	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10121928	0.81[EUR][1000 genomes]
rs10122619	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10124705	0.81[EUR][1000 genomes]
rs10124796	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10992160	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10992163	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10992175	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12340061	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12344469	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12349001	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12349258	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1919104	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28477960	0.81[EUR][1000 genomes]
rs56266486	0.81[EUR][1000 genomes]
rs57496363	0.81[EUR][1000 genomes]
rs57862149	0.81[EUR][1000 genomes]
rs58964193	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59195968	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59917975	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60351369	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61266489	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7027147	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7033888	0.81[EUR][1000 genomes]
rs7035117	0.89[CHB][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7036958	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7043019	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7045073	0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7045603	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73519176	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73520858	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73520881	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73520889	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73522907	0.81[EUR][1000 genomes]
rs73522929	0.81[EUR][1000 genomes]
rs7851412	0.81[EUR][1000 genomes]
rs7856148	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7863425	1.00[CHB][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7867659	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
4	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv831653	chr9:94692454-94867542	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10115262	SPTLC1	cis	multi-tissue	Pritchard
rs10115262	SPTLC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94695800-94702400	Enhancers	Fetal Lung	lung
2	chr9:94698000-94708200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:94698400-94707000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:94698400-94707600	Weak transcription	Fetal Intestine Small	intestine
5	chr9:94698600-94708200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr9:94698800-94702800	Weak transcription	Lung	lung
7	chr9:94700800-94707000	Weak transcription	Gastric	stomach
8	chr9:94701000-94702800	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr9:94701000-94702800	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr9:94701000-94703000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr9:94701400-94707800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:94701600-94702400	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr9:94701600-94702800	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr9:94701800-94702400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:94701800-94702400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:94701800-94702400	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr9:94701800-94702400	Genic enhancers	K562	blood
18	chr9:94701800-94702600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr9:94701800-94702600	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr9:94701800-94702800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:94701800-94703000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:94702000-94702400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:94702000-94702600	Enhancers	H1 Cell Line	embryonic stem cell
24	chr9:94702000-94702600	Enhancers	Ovary	ovary
25	chr9:94702000-94702600	Enhancers	Rectal Smooth Muscle	rectum
26	chr9:94702000-94706200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr9:94702200-94702400	Enhancers	Colon Smooth Muscle	Colon
28	chr9:94702200-94702400	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr9:94702200-94702400	Enhancers	Placenta	Placenta
30	chr9:94702200-94702400	Enhancers	Right Atrium	heart
31	chr9:94702200-94702600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:94702200-94702800	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr9:94702200-94703000	Genic enhancers	Fetal Stomach	stomach

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