Variant report

Variant	rs72688824
Chromosome Location	chr14:78264733-78264734
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	chr14:78227205..78229069-chr14:78264195..78266638,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100603	Chromatin interaction
ENSG00000197734	Chromatin interaction
ENSG00000268208	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10162548	1.00[ASN][1000 genomes]
rs11621162	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622176	1.00[ASN][1000 genomes]
rs11622293	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622411	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622449	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11623898	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624052	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624063	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625029	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625607	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625647	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11626900	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11628795	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17752726	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825434	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825458	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825620	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032745	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112135	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28445066	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28541608	1.00[ASN][1000 genomes]
rs28607620	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28651563	1.00[ASN][1000 genomes]
rs4461000	1.00[ASN][1000 genomes]
rs4464012	1.00[ASN][1000 genomes]
rs45444693	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45465691	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4996830	1.00[ASN][1000 genomes]
rs55636050	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55922310	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55995783	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56003103	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56025136	0.88[ASN][1000 genomes]
rs56060413	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56065232	1.00[ASN][1000 genomes]
rs56109335	0.94[ASN][1000 genomes]
rs57615727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58171071	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59200674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6494	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140838	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7146719	1.00[ASN][1000 genomes]
rs7148685	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7155062	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685214	1.00[ASN][1000 genomes]
rs72685216	1.00[ASN][1000 genomes]
rs72685219	1.00[ASN][1000 genomes]
rs72685222	1.00[ASN][1000 genomes]
rs72685223	1.00[ASN][1000 genomes]
rs72685230	1.00[ASN][1000 genomes]
rs72685232	1.00[ASN][1000 genomes]
rs72685244	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685260	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685273	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685280	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685281	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685293	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685296	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685300	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687205	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687216	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687217	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687218	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687222	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687228	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687229	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687246	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687250	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687251	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687261	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8015313	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv2754594	chr14:78222798-78275549	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs72688824	SPTLC2	cis	Nerve Tibial	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78253800-78266200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:78259600-78266200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr14:78262200-78265800	Weak transcription	K562	blood
4	chr14:78262200-78266000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr14:78262200-78266000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr14:78262400-78265800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr14:78262400-78266000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr14:78262400-78266000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr14:78262400-78266000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr14:78262400-78266000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr14:78262400-78266000	Weak transcription	NH-A	brain
12	chr14:78262400-78266200	Weak transcription	HMEC	breast
13	chr14:78262400-78266200	Weak transcription	NHDF-Ad	bronchial
14	chr14:78262600-78265800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr14:78262600-78266000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr14:78262600-78266000	Weak transcription	Osteobl	bone
17	chr14:78262600-78266200	Weak transcription	NHLF	lung
18	chr14:78263000-78265800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr14:78263000-78266000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr14:78263000-78266000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr14:78263000-78266000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr14:78263000-78266000	Weak transcription	Adipose Nuclei	Adipose
23	chr14:78263000-78266000	Weak transcription	A549	lung
24	chr14:78263000-78266000	Weak transcription	NHEK	skin
25	chr14:78263000-78266200	Weak transcription	Stomach Mucosa	stomach
26	chr14:78263000-78266200	Weak transcription	HSMMtube	muscle
27	chr14:78263200-78266200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr14:78263200-78266200	Weak transcription	Psoas Muscle	Psoas
29	chr14:78263400-78266000	Weak transcription	Placenta	Placenta
30	chr14:78263400-78266000	Weak transcription	GM12878-XiMat	blood
31	chr14:78263800-78266000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr14:78264000-78266000	Weak transcription	HepG2	liver
33	chr14:78264600-78266000	Weak transcription	Hela-S3	cervix

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