Variant report

Variant	rs4714140
Chromosome Location	chr6:38254926-38254927
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1475761	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs1931767	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs228181	1.00[CEU][hapmap]
rs228182	0.95[CEU][hapmap]
rs228184	0.90[CEU][hapmap]
rs228185	0.95[CEU][hapmap]
rs228187	0.95[CEU][hapmap]
rs4711529	0.89[EUR][1000 genomes]
rs4711533	0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4714136	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs4714144	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6905637	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6922620	0.95[CEU][hapmap]
rs7760807	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9349067	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9380737	0.85[CEU][hapmap]
rs9462424	0.81[EUR][1000 genomes]
rs9462425	0.84[EUR][1000 genomes]
rs9470847	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs9470848	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs9470849	0.89[EUR][1000 genomes]
rs9470850	0.91[YRI][hapmap]
rs9470851	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs9470856	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];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	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4714140	SPTLC3	trans	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38208200-38255000	Weak transcription	Ovary	ovary
2	chr6:38223600-38256000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:38224400-38267600	Weak transcription	Primary T cells from cord blood	blood
4	chr6:38224600-38255200	Weak transcription	Primary B cells from cord blood	blood
5	chr6:38224800-38256400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:38225000-38255800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:38226400-38258000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr6:38226600-38256600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr6:38226600-38257000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:38230800-38256000	Weak transcription	Right Atrium	heart
11	chr6:38230800-38257800	Weak transcription	Pancreas	Pancrea
12	chr6:38238200-38257000	Weak transcription	Aorta	Aorta
13	chr6:38238400-38255000	Weak transcription	Lung	lung
14	chr6:38238400-38258200	Weak transcription	Left Ventricle	heart
15	chr6:38238600-38258000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr6:38239400-38257800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:38239400-38259200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:38239800-38257600	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr6:38240000-38257800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:38241600-38258200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:38243400-38257200	Weak transcription	Liver	Liver
22	chr6:38247200-38257800	Weak transcription	Fetal Kidney	kidney
23	chr6:38248000-38255600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:38248400-38258400	Weak transcription	Colon Smooth Muscle	Colon
25	chr6:38248800-38257400	Weak transcription	Fetal Heart	heart
26	chr6:38249000-38256000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr6:38249000-38256000	Weak transcription	Brain Substantia Nigra	brain
28	chr6:38249000-38257600	Weak transcription	Brain Anterior Caudate	brain
29	chr6:38249000-38258200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr6:38249200-38257800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr6:38249200-38258000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:38249200-38258000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:38249200-38258400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:38249200-38275600	Weak transcription	Fetal Brain Male	brain
35	chr6:38249600-38255800	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:38249600-38255800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr6:38250600-38257600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:38250600-38258200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr6:38252200-38257600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:38252200-38257600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:38252400-38256000	Weak transcription	Stomach Mucosa	stomach
42	chr6:38252400-38257800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:38253000-38257400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:38253200-38256200	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr6:38253200-38256800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr6:38253200-38257200	Weak transcription	Adipose Nuclei	Adipose
47	chr6:38253200-38257600	Weak transcription	Fetal Intestine Large	intestine
48	chr6:38253400-38255800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr6:38253400-38256000	Strong transcription	Primary B cells from peripheral blood	blood
50	chr6:38253600-38256400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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