Variant report

Variant	rs12339869
Chromosome Location	chr9:94804719-94804720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr9:94803704-94804998	K562	blood:	n/a	n/a
2	MAFK	chr9:94804660-94804873	HepG2	liver:	n/a	chr9:94804740-94804755
3	MAFK	chr9:94804645-94804852	Hela-S3	cervix:	n/a	chr9:94804740-94804755
4	MAFK	chr9:94804622-94804881	HepG2	liver:	n/a	chr9:94804740-94804755
5	SETDB1	chr9:94803148-94804797	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:94803091..94807436-chr9:94808499..94811192,5	K562	blood:
2	chr9:94800752..94804728-chr9:94805070..94807869,3	K562	blood:

Variant related genes	Relation type
SPTLC1	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10119866	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236475	1.00[JPT][hapmap]
rs12343645	1.00[CHB][hapmap]
rs12343647	1.00[CHB][hapmap]
rs28667175	0.86[ASN][1000 genomes]
rs4560856	1.00[CHB][hapmap]
rs57310547	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60568227	0.86[ASN][1000 genomes]
rs6479406	1.00[CHB][hapmap]
rs7858974	1.00[JPT][hapmap]
rs7869291	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv982320	chr9:94799706-94821700	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12339869	SPTLC1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94791400-94805400	Weak transcription	Psoas Muscle	Psoas
2	chr9:94793600-94805400	Weak transcription	Small Intestine	intestine
3	chr9:94795600-94805400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:94797000-94805400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:94798000-94805600	Weak transcription	Stomach Mucosa	stomach
6	chr9:94800400-94805400	Weak transcription	Hela-S3	cervix
7	chr9:94801000-94805400	Weak transcription	Esophagus	oesophagus
8	chr9:94801000-94805400	Weak transcription	Pancreas	Pancrea
9	chr9:94801000-94805400	Weak transcription	Right Ventricle	heart
10	chr9:94801000-94805400	Weak transcription	Spleen	Spleen
11	chr9:94801200-94805000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:94801200-94805200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:94801200-94805400	Weak transcription	Brain Angular Gyrus	brain
14	chr9:94801200-94805400	Weak transcription	Gastric	stomach
15	chr9:94801200-94805400	Weak transcription	Lung	lung
16	chr9:94801200-94805400	Weak transcription	HSMMtube	muscle
17	chr9:94801400-94805400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:94802800-94810000	Strong transcription	Fetal Muscle Trunk	muscle
19	chr9:94803000-94806000	ZNF genes & repeats	Fetal Muscle Leg	muscle
20	chr9:94803000-94806200	ZNF genes & repeats	Fetal Lung	lung
21	chr9:94803000-94806800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr9:94803000-94807000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:94803000-94807200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr9:94803000-94807400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:94803000-94807400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:94803200-94804800	ZNF genes & repeats	Brain Germinal Matrix	brain
27	chr9:94803200-94804800	ZNF genes & repeats	K562	blood
28	chr9:94803200-94805600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:94803200-94805800	ZNF genes & repeats	NHDF-Ad	bronchial
30	chr9:94803200-94806000	ZNF genes & repeats	Fetal Brain Female	brain
31	chr9:94803200-94806200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:94803200-94806800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
33	chr9:94803200-94807200	ZNF genes & repeats	Primary B cells from cord blood	blood
34	chr9:94803200-94807200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
35	chr9:94803200-94807400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr9:94803200-94809600	Strong transcription	A549	lung
37	chr9:94803200-94810400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:94803200-94813000	Strong transcription	HSMM	muscle
39	chr9:94803400-94807600	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr9:94803400-94821200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr9:94803600-94804800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
42	chr9:94803600-94805000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
43	chr9:94803600-94805600	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
44	chr9:94803600-94806000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr9:94803800-94804800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
46	chr9:94803800-94804800	ZNF genes & repeats	NHLF	lung
47	chr9:94803800-94805000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr9:94803800-94805000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
49	chr9:94803800-94805200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr9:94803800-94805400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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