Variant report

Variant	rs56060413
Chromosome Location	chr14:78177413-78177414
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:77934304..77936307-chr14:78175272..78177718,2	K562	blood:
2	chr14:77934807..77937271-chr14:78175752..78177718,2	K562	blood:

Variant related genes	Relation type
ENSG00000100591	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10162548	1.00[ASN][1000 genomes]
rs11621162	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11621593	0.87[AFR][1000 genomes]
rs11622176	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622293	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622449	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11623898	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624052	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624063	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625029	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625607	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625647	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11626900	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11628795	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17752726	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825434	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825458	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825620	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032745	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2111829	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2112135	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28445066	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28541608	1.00[ASN][1000 genomes]
rs28607620	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28651563	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4461000	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4464012	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45444693	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45465691	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4996830	1.00[ASN][1000 genomes]
rs55636050	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55922310	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55995783	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56003103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56025136	0.88[ASN][1000 genomes]
rs56065232	1.00[ASN][1000 genomes]
rs56109335	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56339806	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57615727	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58171071	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59200674	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493	0.87[AFR][1000 genomes]
rs6494	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140838	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7146719	1.00[ASN][1000 genomes]
rs7148685	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7155062	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685214	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685216	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685219	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685222	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685223	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685230	1.00[ASN][1000 genomes]
rs72685232	1.00[ASN][1000 genomes]
rs72685238	0.87[AFR][1000 genomes]
rs72685244	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685246	0.87[AFR][1000 genomes]
rs72685260	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685273	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685293	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685296	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685297	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72685300	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685302	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72687205	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687216	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687217	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687218	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687222	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687223	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72687228	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687229	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687246	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687247	0.87[AFR][1000 genomes]
rs72687250	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687251	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687261	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72688824	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8015313	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[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	esv2758362	chr14:78074180-78262572	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv2759998	chr14:78074180-78262572	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	esv2757575	chr14:78104897-78212462	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv34940	chr14:78104897-78222798	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv521287	chr14:78108003-78211225	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv520021	chr14:78152921-78208294	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56060413	SPTLC2	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78175200-78177600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr14:78175400-78177600	Weak transcription	Esophagus	oesophagus
3	chr14:78175400-78177600	Weak transcription	Left Ventricle	heart
4	chr14:78175400-78180400	Weak transcription	Gastric	stomach
5	chr14:78175600-78177600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr14:78175600-78180400	Weak transcription	Aorta	Aorta
7	chr14:78175600-78182200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr14:78175800-78177600	Weak transcription	Fetal Stomach	stomach
9	chr14:78175800-78177600	Weak transcription	Pancreas	Pancrea
10	chr14:78175800-78177800	Weak transcription	Colonic Mucosa	Colon
11	chr14:78175800-78178000	Weak transcription	Right Ventricle	heart
12	chr14:78175800-78179000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:78176000-78178000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr14:78176000-78179800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr14:78176200-78178000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr14:78176200-78179800	Strong transcription	Primary hematopoietic stem cells	blood
17	chr14:78176200-78185400	Weak transcription	Fetal Heart	heart
18	chr14:78176200-78206000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr14:78176200-78208400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr14:78176200-78224000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr14:78176200-78225400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr14:78176400-78177800	Weak transcription	Fetal Kidney	kidney
23	chr14:78176400-78206200	Strong transcription	Fetal Thymus	thymus
24	chr14:78176400-78223400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr14:78176400-78224200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr14:78176600-78179400	Strong transcription	Lung	lung
27	chr14:78176600-78179800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
28	chr14:78176600-78180000	Strong transcription	NHDF-Ad	bronchial
29	chr14:78176600-78180400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr14:78176600-78181000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr14:78176600-78182000	Strong transcription	Primary T cells from cord blood	blood
32	chr14:78176600-78182400	Strong transcription	HUVEC	blood vessel
33	chr14:78176600-78187200	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr14:78176600-78187200	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr14:78176600-78197400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr14:78176600-78204600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr14:78176600-78205200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr14:78176600-78205400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr14:78176600-78205600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr14:78176600-78205600	Strong transcription	Adipose Nuclei	Adipose
41	chr14:78176600-78205800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr14:78176600-78213200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr14:78176600-78223200	Strong transcription	Fetal Muscle Leg	muscle
44	chr14:78176600-78224200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr14:78176800-78177600	Weak transcription	Fetal Intestine Small	intestine
46	chr14:78176800-78178600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
47	chr14:78176800-78178800	Strong transcription	Fetal Brain Female	brain
48	chr14:78176800-78179400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr14:78176800-78179600	Strong transcription	Ovary	ovary
50	chr14:78176800-78180600	Strong transcription	Fetal Lung	lung

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