Variant report

Variant	rs12554679
Chromosome Location	chr9:94661115-94661116
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94658826..94661180-chr9:94661410..94663593,2	K562	blood:
2	chr9:94656937..94658928-chr9:94660784..94663442,2	MCF-7	breast:
3	chr9:94647061..94649202-chr9:94659654..94661828,2	MCF-7	breast:
4	chr9:94653069..94655970-chr9:94661069..94663824,3	K562	blood:
5	chr9:94659650..94662569-chr9:94690819..94692460,2	K562	blood:
6	chr9:94661029..94661939-chr9:94710741..94711644,2	K562	blood:
7	chr9:94658208..94667163-chr9:94705322..94714120,17	K562	blood:

Variant related genes	Relation type
ENSG00000169071	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10820921	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs10820922	0.90[CEU][hapmap]
rs10820928	0.91[CEU][hapmap]
rs10820934	0.85[CEU][hapmap]
rs10992161	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs10992224	0.80[CEU][hapmap]
rs1534534	0.82[CEU][hapmap]
rs1892263	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs4744105	0.90[JPT][hapmap]
rs7034006	0.82[CEU][hapmap]
rs7038823	0.82[CEU][hapmap]
rs7857759	0.80[CEU][hapmap]
rs7871522	0.82[CEU][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
rs12554679	SPTLC1	cis	brain	BrainEAC

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94649400-94663200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr9:94650000-94662400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:94651200-94665000	Weak transcription	NHLF	lung
4	chr9:94654000-94661200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:94656400-94661400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:94658000-94663600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:94658000-94667400	Enhancers	Fetal Lung	lung
8	chr9:94658200-94661200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr9:94658200-94661400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:94658200-94662000	Enhancers	Fetal Heart	heart
11	chr9:94658200-94666200	Enhancers	Fetal Kidney	kidney
12	chr9:94658400-94661600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:94658400-94664400	Enhancers	Fetal Intestine Large	intestine
14	chr9:94658400-94664600	Enhancers	Fetal Intestine Small	intestine
15	chr9:94658400-94665800	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr9:94658800-94663400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:94659000-94662400	Enhancers	Fetal Muscle Trunk	muscle
18	chr9:94659000-94663200	Enhancers	Pancreas	Pancrea
19	chr9:94659200-94661600	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr9:94659200-94662800	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr9:94659200-94663000	Enhancers	Gastric	stomach
22	chr9:94659200-94663000	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr9:94659200-94663400	Enhancers	Fetal Muscle Leg	muscle
24	chr9:94659200-94665400	Enhancers	Ovary	ovary
25	chr9:94659600-94661200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr9:94659600-94662600	Enhancers	Rectal Smooth Muscle	rectum
27	chr9:94659600-94663200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:94659600-94665600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr9:94659600-94668400	Enhancers	Colon Smooth Muscle	Colon
30	chr9:94659800-94663600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:94660000-94661400	Enhancers	Esophagus	oesophagus
32	chr9:94660000-94661600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr9:94660000-94662000	Weak transcription	Left Ventricle	heart
34	chr9:94660200-94663400	Enhancers	Placenta	Placenta
35	chr9:94660200-94663800	Enhancers	Duodenum Mucosa	Duodenum
36	chr9:94660200-94666200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr9:94660400-94661200	Genic enhancers	Fetal Stomach	stomach
38	chr9:94660400-94662400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr9:94660400-94662600	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr9:94660400-94662800	Bivalent Enhancer	Stomach Mucosa	stomach
41	chr9:94660400-94663400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr9:94660600-94661600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:94660600-94662400	Flanking Active TSS	K562	blood
44	chr9:94660600-94663000	Enhancers	Fetal Thymus	thymus
45	chr9:94660800-94661200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr9:94660800-94661600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr9:94660800-94662200	Enhancers	H9 Cell Line	embryonic stem cell
48	chr9:94660800-94662200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
49	chr9:94660800-94662400	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr9:94660800-94662400	Enhancers	Brain Hippocampus Middle	brain

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