Variant report

Variant	rs28719093
Chromosome Location	chr14:77997204-77997205
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10151907	1.00[ASN][1000 genomes]
rs17105922	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17105930	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17105935	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17105954	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28417590	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28527479	1.00[ASN][1000 genomes]
rs28584839	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28608714	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28628767	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28677959	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28708472	1.00[ASN][1000 genomes]
rs28714070	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55732483	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56138064	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56192928	0.94[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	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7145386	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7159683	0.84[EUR][1000 genomes]
rs73303254	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74063289	1.00[ASN][1000 genomes]
rs8018049	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8019658	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9323645	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9323647	0.82[EUR][1000 genomes]
rs9806055	0.84[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	nsv85432	chr14:77995986-78001276	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28719093	SPTLC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 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	chr14:77972000-78018000	Weak transcription	Hela-S3	cervix
3	chr14:77978000-78013400	Weak transcription	NHDF-Ad	bronchial
4	chr14:77978600-78014600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr14:77978800-78042200	Weak transcription	Fetal Brain Male	brain
6	chr14:77979000-78003800	Weak transcription	K562	blood
7	chr14:77979000-78009400	Weak transcription	Stomach Mucosa	stomach
8	chr14:77979000-78013800	Weak transcription	Pancreas	Pancrea
9	chr14:77982800-77999800	Weak transcription	A549	lung
10	chr14:77985200-78008800	Weak transcription	Gastric	stomach
11	chr14:77985200-78014800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr14:77985400-78007800	Weak transcription	Colon Smooth Muscle	Colon
13	chr14:77985400-78015000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr14:77985600-78007400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr14:77986200-78013800	Weak transcription	Esophagus	oesophagus
16	chr14:77986800-78008600	Weak transcription	Brain Germinal Matrix	brain
17	chr14:77987400-77999400	Weak transcription	Fetal Intestine Small	intestine
18	chr14:77987400-78009200	Weak transcription	Aorta	Aorta
19	chr14:77987400-78021000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr14:77987600-78010200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr14:77987600-78010600	Weak transcription	Left Ventricle	heart
22	chr14:77987800-77997400	Weak transcription	Brain Angular Gyrus	brain
23	chr14:77987800-77999400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr14:77987800-78007200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr14:77987800-78008800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:77987800-78008800	Weak transcription	Fetal Thymus	thymus
27	chr14:77987800-78013400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr14:77987800-78013600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr14:77987800-78013800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr14:77987800-78014600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr14:77987800-78014600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr14:77987800-78014800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr14:77987800-78015000	Weak transcription	Thymus	Thymus
34	chr14:77987800-78015600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr14:77987800-78060000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr14:77988000-78000400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr14:77988000-78000400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr14:77988000-78001000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr14:77988000-78001000	Weak transcription	Fetal Intestine Large	intestine
40	chr14:77988000-78003800	Weak transcription	Fetal Kidney	kidney
41	chr14:77988000-78007800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr14:77988000-78007800	Weak transcription	Brain Anterior Caudate	brain
43	chr14:77988000-78007800	Weak transcription	Brain Substantia Nigra	brain
44	chr14:77988000-78008200	Weak transcription	Fetal Muscle Leg	muscle
45	chr14:77988000-78008800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr14:77988000-78008800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr14:77988000-78009000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr14:77988000-78010200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr14:77988000-78010600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr14:77988000-78010800	Weak transcription	Dnd41	blood

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