Variant report

Variant	rs55636050
Chromosome Location	chr14:78269686-78269687
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:78269397..78271453-chr14:78289633..78292223,2	K562	blood:
2	chr14:78269599..78272044-chr14:78273167..78277350,3	K562	blood:
3	chr14:78223413..78230716-chr14:78265065..78269735,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100603	Chromatin interaction
ENSG00000268208	Chromatin interaction
ENSG00000197734	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	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622449	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11623898	0.89[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];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625029	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625607	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625647	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11626900	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11628795	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17752726	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825434	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825458	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825620	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032745	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112135	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28445066	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28541608	1.00[ASN][1000 genomes]
rs28607620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4996830	1.00[ASN][1000 genomes]
rs55922310	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55995783	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56003103	0.89[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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58171071	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59200674	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6494	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140838	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7146719	1.00[ASN][1000 genomes]
rs7148685	0.89[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	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685280	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685281	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685293	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685296	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685300	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687205	0.89[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	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687222	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687228	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687229	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687246	0.82[AMR][1000 genomes];0.95[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];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687261	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72688824	1.00[AMR][1000 genomes];0.98[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
rs55636050	SPTLC2	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78267000-78270400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:78267200-78270200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr14:78267200-78270400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr14:78267200-78270600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr14:78267200-78270800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr14:78267200-78271800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr14:78267200-78272400	Weak transcription	Left Ventricle	heart
8	chr14:78267200-78284800	Weak transcription	Brain Angular Gyrus	brain
9	chr14:78267200-78285200	Weak transcription	Colon Smooth Muscle	Colon
10	chr14:78267200-78285200	Weak transcription	Fetal Stomach	stomach
11	chr14:78267200-78285400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr14:78267200-78285400	Weak transcription	Lung	lung
13	chr14:78267200-78288200	Weak transcription	Spleen	Spleen
14	chr14:78267200-78288800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr14:78267200-78304200	Weak transcription	HSMMtube	muscle
16	chr14:78267200-78310800	Weak transcription	Esophagus	oesophagus
17	chr14:78267400-78269800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr14:78267400-78270000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr14:78267400-78270400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr14:78267400-78270400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr14:78267400-78272800	Weak transcription	Stomach Mucosa	stomach
22	chr14:78267400-78285000	Weak transcription	Brain Hippocampus Middle	brain
23	chr14:78267400-78285000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr14:78267400-78285200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr14:78267400-78285400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr14:78267600-78285000	Weak transcription	Primary T cells from cord blood	blood
27	chr14:78267600-78285400	Weak transcription	Brain Substantia Nigra	brain
28	chr14:78267800-78285400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr14:78268800-78272600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr14:78268800-78272800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr14:78269400-78269800	Enhancers	K562	blood
32	chr14:78269600-78270000	Enhancers	Psoas Muscle	Psoas
33	chr14:78269600-78270000	Enhancers	HepG2	liver

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