Variant report

Variant	rs2299914
Chromosome Location	chr14:78013435-78013436
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12101129	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12586959	0.95[ASN][1000 genomes]
rs12589478	0.90[ASN][1000 genomes]
rs17105949	0.95[ASN][1000 genomes]
rs2284230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299911	0.92[ASN][1000 genomes]
rs2299912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28482839	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28654332	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28676801	0.92[ASN][1000 genomes]
rs28716286	0.92[ASN][1000 genomes]
rs34359219	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55949800	0.95[ASN][1000 genomes]
rs56208416	0.88[ASN][1000 genomes]
rs61990763	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61992441	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72683251	0.81[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
rs2299914	SPTLC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 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	chr14:77978600-78014600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr14:77978800-78042200	Weak transcription	Fetal Brain Male	brain
5	chr14:77979000-78013800	Weak transcription	Pancreas	Pancrea
6	chr14:77985200-78014800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr14:77985400-78015000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr14:77986200-78013800	Weak transcription	Esophagus	oesophagus
9	chr14:77987400-78021000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr14:77987800-78013600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr14:77987800-78013800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr14:77987800-78014600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr14:77987800-78014600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr14:77987800-78014800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr14:77987800-78015000	Weak transcription	Thymus	Thymus
16	chr14:77987800-78015600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr14:77987800-78060000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr14:77988000-78013800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr14:77988000-78013800	Weak transcription	Colonic Mucosa	Colon
20	chr14:77988000-78014600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr14:77988000-78014800	Weak transcription	HMEC	breast
22	chr14:77988000-78015200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr14:77988000-78015600	Weak transcription	Right Ventricle	heart
24	chr14:77988400-78013800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr14:77988400-78029400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr14:77997800-78018800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr14:78001400-78014000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr14:78001800-78014000	Weak transcription	Fetal Intestine Small	intestine
29	chr14:78002000-78014800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr14:78002000-78015000	Weak transcription	Lung	lung
31	chr14:78002200-78014400	Weak transcription	A549	lung
32	chr14:78002200-78020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr14:78002400-78013600	Weak transcription	NHEK	skin
34	chr14:78004000-78014800	Weak transcription	Ovary	ovary
35	chr14:78004600-78014400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr14:78006800-78019000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr14:78008200-78015600	Weak transcription	NHLF	lung
38	chr14:78008200-78019000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr14:78009200-78013600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr14:78009200-78014800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr14:78009200-78015400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr14:78009400-78013600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr14:78009600-78013600	Weak transcription	Fetal Muscle Leg	muscle
44	chr14:78009600-78014800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr14:78009600-78015600	Weak transcription	Brain Germinal Matrix	brain
46	chr14:78009600-78019400	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr14:78009600-78021200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr14:78009600-78030000	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr14:78009800-78013800	Weak transcription	Aorta	Aorta
50	chr14:78009800-78014800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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