Variant report

Variant	rs12590866
Chromosome Location	chr14:78022585-78022586
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:77786580..77789225-chr14:78021579..78023243,2	MCF-7	breast:
2	chr14:77923636..77926196-chr14:78022386..78024984,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100577	Chromatin interaction
ENSG00000100591	Chromatin interaction
ENSG00000009830	Chromatin interaction
ENSG00000151445	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11159275	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11621440	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629330	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17751727	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2003633	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2012998	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272587	0.94[ASN][1000 genomes]
rs2272588	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2886131	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34153615	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35964784	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36063635	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36111947	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56202833	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs56225479	0.94[ASN][1000 genomes]
rs60221235	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7153686	0.89[ASN][1000 genomes]
rs741850	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8003639	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8003812	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8014527	0.94[ASN][1000 genomes]

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	nsv832835	chr14:77906706-78095207	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1053810	chr14:77987871-78148320	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1051554	chr14:78004196-78122980	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12590866	SPTLC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77970200-78047200	Weak transcription	Fetal Heart	heart
2	chr14:77978800-78042200	Weak transcription	Fetal Brain Male	brain
3	chr14:77987800-78060000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr14:77988400-78029400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr14:78009600-78030000	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr14:78009800-78050800	Weak transcription	Psoas Muscle	Psoas
7	chr14:78010000-78029800	Strong transcription	Primary T cells from cord blood	blood
8	chr14:78010200-78026800	Weak transcription	Stomach Mucosa	stomach
9	chr14:78010400-78030000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr14:78010600-78025000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr14:78011000-78031800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr14:78011200-78045800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr14:78011400-78037400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr14:78013200-78030600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr14:78013200-78066200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr14:78013400-78025800	Strong transcription	HSMM	muscle
17	chr14:78013600-78026200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr14:78015200-78023200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr14:78015200-78024400	Strong transcription	HUVEC	blood vessel
20	chr14:78016000-78023800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr14:78016000-78040000	Weak transcription	Pancreas	Pancrea
22	chr14:78016200-78023200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr14:78016200-78037200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr14:78016400-78023200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr14:78016400-78061000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr14:78017800-78024200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr14:78018000-78029400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr14:78018600-78044200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr14:78018800-78023200	Weak transcription	NHDF-Ad	bronchial
30	chr14:78018800-78023400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr14:78018800-78031800	Weak transcription	Ovary	ovary
32	chr14:78018800-78041600	Weak transcription	A549	lung
33	chr14:78018800-78047000	Weak transcription	Placenta	Placenta
34	chr14:78019400-78022800	Strong transcription	Fetal Stomach	stomach
35	chr14:78019400-78025000	Strong transcription	Osteobl	bone
36	chr14:78019400-78040800	Weak transcription	Hela-S3	cervix
37	chr14:78019600-78022600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr14:78019800-78029600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr14:78019800-78030600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr14:78020000-78024600	Genic enhancers	Primary B cells from peripheral blood	blood
41	chr14:78020000-78025000	Strong transcription	Fetal Muscle Trunk	muscle
42	chr14:78020000-78030400	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr14:78020200-78022600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr14:78020200-78024400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr14:78020200-78024400	Genic enhancers	Primary hematopoietic stem cells	blood
46	chr14:78020200-78025000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr14:78020200-78025000	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr14:78020200-78028800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr14:78020400-78022600	Enhancers	Brain Angular Gyrus	brain
50	chr14:78020400-78023400	Enhancers	Brain Substantia Nigra	brain

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