Variant report

Variant	rs56264628
Chromosome Location	chr14:78034779-78034780
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	chr14:78033681..78035724-chr14:78039789..78042606,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10143360	0.91[ASN][1000 genomes]
rs12431896	1.00[AFR][1000 genomes]
rs12433198	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12433737	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs176895	1.00[AFR][1000 genomes]
rs176896	1.00[AFR][1000 genomes]
rs176899	1.00[AFR][1000 genomes]
rs176906	1.00[AFR][1000 genomes]
rs176911	1.00[AFR][1000 genomes]
rs17751876	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs17751917	1.00[AFR][1000 genomes]
rs17751980	1.00[AFR][1000 genomes]
rs17751993	1.00[AFR][1000 genomes]
rs17752165	1.00[AFR][1000 genomes]
rs17825014	1.00[AFR][1000 genomes]
rs2178877	1.00[AFR][1000 genomes]
rs2299918	0.80[AMR][1000 genomes]
rs2364578	1.00[AFR][1000 genomes]
rs2886132	1.00[AFR][1000 genomes]
rs4497612	1.00[AFR][1000 genomes]
rs55697089	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55776552	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55799811	1.00[AFR][1000 genomes]
rs56230840	0.91[ASN][1000 genomes]
rs56286233	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73303267	0.91[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	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
4	esv1794863	chr14:78024926-78048715	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56264628	SPTLC2	cis	Nerve Tibial	GTEx

Chromatin state (count:121 , 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	chr14:77978800-78042200	Weak transcription	Fetal Brain Male	brain
3	chr14:77987800-78060000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr14:78009800-78050800	Weak transcription	Psoas Muscle	Psoas
5	chr14:78011200-78045800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr14:78011400-78037400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr14:78013200-78066200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr14:78016000-78040000	Weak transcription	Pancreas	Pancrea
9	chr14:78016200-78037200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr14:78016400-78061000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr14:78018600-78044200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr14:78018800-78041600	Weak transcription	A549	lung
13	chr14:78018800-78047000	Weak transcription	Placenta	Placenta
14	chr14:78019400-78040800	Weak transcription	Hela-S3	cervix
15	chr14:78021600-78047000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr14:78021800-78041200	Weak transcription	Small Intestine	intestine
17	chr14:78021800-78061000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr14:78021800-78068400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr14:78021800-78071600	Weak transcription	Colon Smooth Muscle	Colon
20	chr14:78022000-78060800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr14:78022200-78041800	Weak transcription	Gastric	stomach
22	chr14:78022400-78035200	Weak transcription	Fetal Kidney	kidney
23	chr14:78022400-78040200	Weak transcription	Aorta	Aorta
24	chr14:78022400-78047200	Weak transcription	Brain Germinal Matrix	brain
25	chr14:78022400-78049000	Weak transcription	Right Ventricle	heart
26	chr14:78022400-78055000	Weak transcription	Colonic Mucosa	Colon
27	chr14:78022600-78040000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr14:78022600-78041800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr14:78023000-78037000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr14:78023600-78040000	Weak transcription	HepG2	liver
31	chr14:78024000-78040600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr14:78024000-78046400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr14:78024200-78035600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr14:78024200-78036800	Weak transcription	Brain Angular Gyrus	brain
35	chr14:78024200-78036800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr14:78024200-78041000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr14:78024200-78041800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr14:78024200-78046800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr14:78024200-78047200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr14:78024400-78041600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr14:78025000-78035400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr14:78026200-78045600	Weak transcription	Fetal Lung	lung
43	chr14:78028000-78041800	Weak transcription	Esophagus	oesophagus
44	chr14:78028200-78040000	Weak transcription	Spleen	Spleen
45	chr14:78028200-78041200	Weak transcription	NHDF-Ad	bronchial
46	chr14:78028400-78041000	Weak transcription	Fetal Brain Female	brain
47	chr14:78028400-78041800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr14:78028600-78047200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr14:78029200-78035200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr14:78029400-78035400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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