Variant report

Variant	rs9774945
Chromosome Location	chr9:94710847-94710848
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10118409	0.89[YRI][hapmap]
rs10761137	0.83[CEU][hapmap];0.83[MEX][hapmap]
rs10761138	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12340044	0.81[JPT][hapmap]
rs12341791	0.82[YRI][hapmap]
rs1316268	0.85[ASN][1000 genomes]
rs1534534	0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs1609292	0.83[CEU][hapmap]
rs1881391	0.92[CEU][hapmap]
rs1892268	0.84[GIH][hapmap];0.91[MEX][hapmap]
rs2297568	0.84[GIH][hapmap];0.91[MEX][hapmap]
rs2312739	0.83[ASN][1000 genomes]
rs4430151	0.84[CEU][hapmap]
rs6479383	0.84[CEU][hapmap]
rs6479387	0.92[CEU][hapmap]
rs6479389	0.92[CEU][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes]
rs7023075	0.81[JPT][hapmap]
rs7033888	0.85[YRI][hapmap]
rs7034006	0.82[TSI][hapmap]
rs7037255	0.87[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7038017	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7038397	0.82[TSI][hapmap]
rs7038823	0.84[EUR][1000 genomes]
rs7041193	0.84[GIH][hapmap];0.91[MEX][hapmap]
rs7042102	0.88[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap]
rs7047326	0.82[EUR][1000 genomes]
rs7048699	0.92[CEU][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7850309	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7852032	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7863167	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7867072	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7871522	0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv982625	chr9:94702344-94712887	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9774945	SPTLC1	cis	lymphoblastoid	seeQTL
rs9774945	SPTLC1	cis	parietal	SCAN
rs9774945	C9orf170	cis	cerebellum	SCAN
rs9774945	ZNF484	cis	cerebellum	SCAN
rs9774945	SPTLC1	cis	multi-tissue	Pritchard

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94709200-94713200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:94709800-94713200	Active TSS	Fetal Kidney	kidney
3	chr9:94710000-94712800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:94710000-94712800	Active TSS	K562	blood
5	chr9:94710000-94714000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:94710200-94711000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
7	chr9:94710200-94713000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr9:94710200-94713200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:94710200-94713200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr9:94710200-94713200	Active TSS	Colon Smooth Muscle	Colon
11	chr9:94710400-94711000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
12	chr9:94710400-94711000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:94710400-94711000	Bivalent Enhancer	Fetal Brain Male	brain
14	chr9:94710400-94711000	Active TSS	Right Atrium	heart
15	chr9:94710400-94711200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr9:94710400-94711200	Active TSS	Fetal Heart	heart
17	chr9:94710400-94711200	Bivalent/Poised TSS	NHLF	lung
18	chr9:94710400-94711400	Bivalent/Poised TSS	Colonic Mucosa	Colon
19	chr9:94710400-94711800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
20	chr9:94710400-94711800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:94710400-94712000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
22	chr9:94710400-94712000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
23	chr9:94710400-94712200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:94710400-94712200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:94710400-94712600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
26	chr9:94710400-94713000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:94710400-94713200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:94710400-94713200	Active TSS	Fetal Lung	lung
29	chr9:94710400-94713400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
30	chr9:94710600-94711000	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:94710600-94711000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:94710600-94711000	Flanking Active TSS	Gastric	stomach
33	chr9:94710600-94711000	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr9:94710600-94711000	Flanking Bivalent TSS/Enh	Hela-S3	cervix
35	chr9:94710600-94711200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:94710600-94711200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
37	chr9:94710600-94711800	Bivalent Enhancer	Liver	Liver
38	chr9:94710600-94711800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
39	chr9:94710600-94711800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
40	chr9:94710600-94712000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
41	chr9:94710600-94712600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
42	chr9:94710600-94712800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:94710600-94712800	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr9:94710600-94712800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr9:94710600-94713000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr9:94710600-94713200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
47	chr9:94710600-94713200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
48	chr9:94710600-94713200	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr9:94710600-94713400	Active TSS	Ovary	ovary
50	chr9:94710800-94711000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung

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