Variant report

Variant	rs72687229
Chromosome Location	chr14:78222474-78222475
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:78222223-78222687	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:78208675..78210244-chr14:78222102..78225060,2	K562	blood:
2	chr14:78222067..78225484-chr14:78225871..78228638,3	K562	blood:
3	chr14:78221316..78225180-chr14:78225446..78228735,5	MCF-7	breast:

Variant related genes	Relation type
C14orf178	TF binding region
ENSG00000268208	Chromatin interaction
ENSG00000197734	Chromatin interaction
ENSG00000100603	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10162548	1.00[ASN][1000 genomes]
rs11621162	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11621593	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11622176	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622293	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622411	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622449	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11623898	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624052	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624063	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625029	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625607	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11626900	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11628795	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17752726	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825434	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825458	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825620	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032745	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[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];1.00[ASN][1000 genomes]
rs28445066	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28541608	1.00[ASN][1000 genomes]
rs28607620	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28651563	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4461000	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4464012	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45444693	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45465691	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4996830	1.00[ASN][1000 genomes]
rs55636050	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55922310	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55995783	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56003103	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56025136	0.88[ASN][1000 genomes]
rs56060413	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56065232	1.00[ASN][1000 genomes]
rs56109335	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56339806	0.87[AFR][1000 genomes]
rs57615727	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58171071	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59200674	0.92[EUR][1000 genomes];1.00[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];1.00[ASN][1000 genomes]
rs7140838	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7146719	1.00[ASN][1000 genomes]
rs7148685	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7155062	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685214	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685216	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685219	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685222	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685223	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685230	1.00[ASN][1000 genomes]
rs72685232	1.00[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];1.00[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];1.00[ASN][1000 genomes]
rs72685273	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685280	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685281	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685293	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685296	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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];1.00[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];1.00[ASN][1000 genomes]
rs72687216	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687217	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687218	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687222	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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];1.00[ASN][1000 genomes]
rs72687246	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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];1.00[ASN][1000 genomes]
rs72687251	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687261	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72688824	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8015313	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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
rs72687229	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	chr14:78177000-78222600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr14:78177000-78224200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr14:78177200-78223800	Strong transcription	Dnd41	blood
10	chr14:78199000-78225200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr14:78199600-78225000	Weak transcription	Fetal Heart	heart
12	chr14:78201600-78226600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr14:78207400-78223000	Strong transcription	Fetal Thymus	thymus
14	chr14:78207600-78224800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr14:78207600-78225400	Strong transcription	Placenta	Placenta
16	chr14:78209800-78223000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr14:78210000-78223800	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr14:78210600-78222800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr14:78211400-78223400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr14:78211400-78223800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr14:78212800-78222800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr14:78212800-78225600	Weak transcription	Stomach Mucosa	stomach
23	chr14:78214000-78223000	Strong transcription	Fetal Lung	lung
24	chr14:78214200-78222800	Strong transcription	Primary T cells from cord blood	blood
25	chr14:78214200-78226600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr14:78214400-78223600	Strong transcription	Duodenum Mucosa	Duodenum
27	chr14:78215000-78222800	Strong transcription	Fetal Intestine Large	intestine
28	chr14:78215200-78223400	Strong transcription	Fetal Muscle Trunk	muscle
29	chr14:78215400-78223800	Strong transcription	Primary B cells from cord blood	blood
30	chr14:78215600-78223000	Strong transcription	Fetal Brain Female	brain
31	chr14:78216200-78223800	Weak transcription	Colon Smooth Muscle	Colon
32	chr14:78216400-78225000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr14:78216400-78225400	Weak transcription	Esophagus	oesophagus
34	chr14:78216600-78224800	Weak transcription	Pancreas	Pancrea
35	chr14:78216800-78225200	Weak transcription	NHLF	lung
36	chr14:78217000-78225000	Weak transcription	HSMMtube	muscle
37	chr14:78217000-78226600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr14:78217400-78224800	Weak transcription	Brain Substantia Nigra	brain
39	chr14:78217600-78225200	Weak transcription	Gastric	stomach
40	chr14:78217600-78225200	Weak transcription	Spleen	Spleen
41	chr14:78217600-78225400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr14:78217800-78225200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr14:78217800-78225200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr14:78218000-78222600	Weak transcription	Right Atrium	heart
45	chr14:78218000-78225200	Weak transcription	Brain Angular Gyrus	brain
46	chr14:78218000-78226400	Weak transcription	Aorta	Aorta
47	chr14:78218200-78225400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr14:78218200-78226400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr14:78218400-78225000	Weak transcription	Small Intestine	intestine
50	chr14:78218400-78225200	Weak transcription	Left Ventricle	heart

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