Variant report

Variant	rs12340061
Chromosome Location	chr9:94668588-94668589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:94664745..94669992-chr9:94681267..94685780,5	K562	blood:
2	chr9:94667170..94669992-chr9:94682219..94685194,2	K562	blood:
3	chr9:94513749..94516669-chr9:94667565..94670057,2	K562	blood:
4	chr9:94667534..94670775-chr9:94707582..94710553,5	K562	blood:
5	chr9:94668298..94670919-chr9:94728281..94730524,2	K562	blood:
6	chr9:94650894..94652826-chr9:94665751..94669153,3	K562	blood:
7	chr9:94666595..94672238-chr9:94672403..94678372,8	K562	blood:
8	chr9:94645315..94647676-chr9:94666839..94670309,3	K562	blood:
9	chr9:94667321..94670775-chr9:94706336..94711619,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000169071	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10046835	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10114686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10115262	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10118781	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10120655	0.80[ASN][1000 genomes]
rs10122619	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10124796	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10512218	1.00[CEU][hapmap]
rs10512219	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10992160	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992163	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992175	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12341791	1.00[CEU][hapmap]
rs12344469	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12349258	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16907940	1.00[CEU][hapmap]
rs1919104	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58964193	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59195968	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59917975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60351369	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61266489	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7027147	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7035117	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]
rs7036958	0.80[ASN][1000 genomes]
rs7043019	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7045073	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7045602	0.88[GIH][hapmap]
rs7045603	0.80[ASN][1000 genomes]
rs73519176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73520858	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73520881	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73520889	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7856148	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7863425	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7875037	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv3347273	chr9:94666131-94669029	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12340061	SPTLC1	cis	multi-tissue	Pritchard
rs12340061	SPTLC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94662200-94669400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:94664800-94669600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:94665400-94669600	Weak transcription	Ovary	ovary
4	chr9:94665800-94669600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:94667000-94669600	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr9:94667000-94670200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:94667000-94671600	Enhancers	Fetal Heart	heart
8	chr9:94667800-94668600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:94667800-94669000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:94667800-94669000	Active TSS	Rectal Smooth Muscle	rectum
11	chr9:94667800-94672200	Weak transcription	Small Intestine	intestine
12	chr9:94668000-94669000	Flanking Active TSS	Dnd41	blood
13	chr9:94668000-94669200	Active TSS	Duodenum Mucosa	Duodenum
14	chr9:94668000-94670400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:94668000-94671400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:94668200-94668600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr9:94668200-94668600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr9:94668200-94668600	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr9:94668200-94668600	Active TSS	Monocytes-CD14+_RO01746	blood
20	chr9:94668200-94668800	Enhancers	Primary B cells from peripheral blood	blood
21	chr9:94668200-94668800	Active TSS	Primary T cells from cord blood	blood
22	chr9:94668200-94668800	Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr9:94668200-94668800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr9:94668200-94668800	Active TSS	A549	lung
25	chr9:94668200-94669000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:94668200-94669000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
27	chr9:94668200-94669000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr9:94668200-94669000	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr9:94668200-94669000	Bivalent/Poised TSS	Osteobl	bone
30	chr9:94668200-94669200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr9:94668200-94670600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:94668400-94668600	Flanking Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr9:94668400-94668600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
34	chr9:94668400-94668600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
35	chr9:94668400-94668600	Active TSS	Primary monocytes fromperipheralblood	blood
36	chr9:94668400-94668600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr9:94668400-94668600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr9:94668400-94668600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:94668400-94668600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr9:94668400-94668600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:94668400-94668600	Flanking Active TSS	Colonic Mucosa	Colon
42	chr9:94668400-94668600	Flanking Active TSS	Colon Smooth Muscle	Colon
43	chr9:94668400-94668600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr9:94668400-94668600	Active TSS	Fetal Intestine Large	intestine
45	chr9:94668400-94668600	Flanking Active TSS	Fetal Intestine Small	intestine
46	chr9:94668400-94668600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
47	chr9:94668400-94668600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
48	chr9:94668400-94668600	Flanking Active TSS	Fetal Stomach	stomach
49	chr9:94668400-94668600	Active TSS	Left Ventricle	heart
50	chr9:94668400-94668600	Active TSS	Right Ventricle	heart

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