Variant report

Variant	rs11625647
Chromosome Location	chr14:78220575-78220576
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10162548	0.88[ASN][1000 genomes]
rs11621162	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11621593	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11622176	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11622293	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11622411	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11622449	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11623898	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11624052	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11624063	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11625029	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11625607	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11626900	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11628795	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17752726	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17825434	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17825458	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17825620	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2032745	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2111829	0.89[AFR][1000 genomes]
rs2112135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28445066	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28541608	0.88[ASN][1000 genomes]
rs28607620	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28651563	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4461000	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4464012	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs45444693	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs45465691	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4996830	0.88[ASN][1000 genomes]
rs55636050	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55922310	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55995783	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56003103	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56060413	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56065232	0.88[ASN][1000 genomes]
rs56109335	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56339806	0.87[AFR][1000 genomes]
rs57615727	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58171071	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59200674	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6493	0.81[AFR][1000 genomes]
rs6494	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7140838	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7146719	0.88[ASN][1000 genomes]
rs7148685	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7155062	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72685214	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72685216	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72685219	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72685222	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72685223	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72685230	0.88[ASN][1000 genomes]
rs72685232	0.88[ASN][1000 genomes]
rs72685238	0.81[AFR][1000 genomes]
rs72685244	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72685246	0.81[AFR][1000 genomes]
rs72685260	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72685273	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72685280	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72685281	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72685293	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72685296	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72685297	0.92[AFR][1000 genomes]
rs72685300	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72685302	0.92[AFR][1000 genomes]
rs72687205	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72687216	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72687217	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72687218	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72687222	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72687223	0.92[AFR][1000 genomes]
rs72687228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72687229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72687246	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72687247	0.92[AFR][1000 genomes]
rs72687250	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72687251	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72687261	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72688824	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8015313	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	nsv1043788	chr14:78178490-78381190	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11625647	SPTLC2	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78176200-78224000	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr14:78176200-78225400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr14:78176400-78223400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr14:78176400-78224200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr14:78176600-78223200	Strong transcription	Fetal Muscle Leg	muscle
6	chr14:78176600-78224200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr14:78176800-78221800	Strong transcription	Primary B cells from peripheral blood	blood
8	chr14:78176800-78222200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr14:78177000-78222600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr14:78177000-78224200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr14:78177200-78223800	Strong transcription	Dnd41	blood
12	chr14:78177400-78222400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr14:78199000-78225200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr14:78199600-78225000	Weak transcription	Fetal Heart	heart
15	chr14:78201600-78226600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr14:78206800-78221400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr14:78207000-78222000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr14:78207200-78222000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr14:78207400-78223000	Strong transcription	Fetal Thymus	thymus
20	chr14:78207600-78222400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr14:78207600-78224800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr14:78207600-78225400	Strong transcription	Placenta	Placenta
23	chr14:78208400-78221400	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr14:78208800-78221800	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr14:78209600-78221200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:78209600-78221400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr14:78209800-78223000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr14:78210000-78223800	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr14:78210600-78222800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr14:78211200-78221800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr14:78211400-78223400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr14:78211400-78223800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr14:78212000-78221600	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr14:78212800-78222800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr14:78212800-78225600	Weak transcription	Stomach Mucosa	stomach
36	chr14:78213600-78221400	Strong transcription	Adipose Nuclei	Adipose
37	chr14:78214000-78221800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr14:78214000-78223000	Strong transcription	Fetal Lung	lung
39	chr14:78214200-78221400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr14:78214200-78221600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr14:78214200-78221600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr14:78214200-78222000	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr14:78214200-78222800	Strong transcription	Primary T cells from cord blood	blood
44	chr14:78214200-78226600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr14:78214400-78223600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr14:78215000-78222800	Strong transcription	Fetal Intestine Large	intestine
47	chr14:78215200-78221400	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr14:78215200-78221600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr14:78215200-78221600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr14:78215200-78221600	Strong transcription	Hela-S3	cervix

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