Variant report

Variant	rs28608714
Chromosome Location	chr14:78019880-78019881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10151907	1.00[ASN][1000 genomes]
rs17105922	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17105930	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17105935	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17105949	0.85[AFR][1000 genomes]
rs17105954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28417590	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28527479	1.00[ASN][1000 genomes]
rs28584839	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28628767	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28677959	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28708472	1.00[ASN][1000 genomes]
rs28714070	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28719093	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55732483	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55949800	0.88[AFR][1000 genomes]
rs56138064	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56192928	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56276583	1.00[ASN][1000 genomes]
rs56327799	1.00[ASN][1000 genomes]
rs56361144	1.00[ASN][1000 genomes]
rs7144024	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7145386	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7159683	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73303254	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74063289	1.00[ASN][1000 genomes]
rs8018049	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8019658	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9323645	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9323647	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9806055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs28608714	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	chr14:77987400-78021000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr14:77987800-78060000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr14:77988400-78029400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr14:78002200-78020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr14:78009600-78021200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr14:78009600-78030000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr14:78009800-78050800	Weak transcription	Psoas Muscle	Psoas
10	chr14:78010000-78029800	Strong transcription	Primary T cells from cord blood	blood
11	chr14:78010200-78020400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr14:78010200-78026800	Weak transcription	Stomach Mucosa	stomach
13	chr14:78010400-78030000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr14:78010600-78025000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr14:78011000-78020000	Strong transcription	Primary B cells from peripheral blood	blood
16	chr14:78011000-78031800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr14:78011200-78045800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr14:78011400-78037400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr14:78013200-78030600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr14:78013200-78066200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr14:78013400-78025800	Strong transcription	HSMM	muscle
22	chr14:78013600-78026200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr14:78015200-78020400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr14:78015200-78023200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr14:78015200-78024400	Strong transcription	HUVEC	blood vessel
26	chr14:78015800-78020800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr14:78015800-78021200	Weak transcription	Gastric	stomach
28	chr14:78016000-78021200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr14:78016000-78021200	Weak transcription	Right Ventricle	heart
30	chr14:78016000-78021600	Weak transcription	Aorta	Aorta
31	chr14:78016000-78023800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr14:78016000-78040000	Weak transcription	Pancreas	Pancrea
33	chr14:78016200-78020400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr14:78016200-78021000	Weak transcription	Colonic Mucosa	Colon
35	chr14:78016200-78021000	Weak transcription	Left Ventricle	heart
36	chr14:78016200-78021200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr14:78016200-78021200	Weak transcription	Thymus	Thymus
38	chr14:78016200-78023200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr14:78016200-78037200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr14:78016400-78020200	Weak transcription	HMEC	breast
41	chr14:78016400-78020400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr14:78016400-78020400	Weak transcription	Brain Substantia Nigra	brain
43	chr14:78016400-78021000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr14:78016400-78021200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr14:78016400-78021200	Weak transcription	Colon Smooth Muscle	Colon
46	chr14:78016400-78021200	Weak transcription	NHEK	skin
47	chr14:78016400-78021400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr14:78016400-78021400	Weak transcription	Brain Germinal Matrix	brain
49	chr14:78016400-78023200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr14:78016400-78061000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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