Variant report

Variant	rs59721556
Chromosome Location	chr14:78112393-78112394
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12431525	0.93[ASN][1000 genomes]
rs12431896	0.90[ASN][1000 genomes]
rs12433954	0.93[ASN][1000 genomes]
rs12434701	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12436803	0.93[ASN][1000 genomes]
rs176895	0.84[ASN][1000 genomes]
rs176896	0.84[ASN][1000 genomes]
rs176906	0.84[ASN][1000 genomes]
rs176908	0.84[ASN][1000 genomes]
rs176911	0.84[ASN][1000 genomes]
rs176912	0.84[ASN][1000 genomes]
rs17752165	0.90[ASN][1000 genomes]
rs17752262	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17825229	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17825235	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2886122	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35389286	0.93[ASN][1000 genomes]
rs55799811	0.93[ASN][1000 genomes]
rs58312042	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	esv2757575	chr14:78104897-78212462	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	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
7	nsv521287	chr14:78108003-78211225	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59721556	SPTLC2	cis	Nerve Tibial	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78108800-78118000	Weak transcription	Psoas Muscle	Psoas
2	chr14:78109000-78113400	Weak transcription	Fetal Intestine Large	intestine
3	chr14:78109000-78113800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr14:78111400-78112800	Enhancers	Placenta	Placenta
5	chr14:78112000-78112400	Enhancers	Duodenum Mucosa	Duodenum
6	chr14:78112000-78112400	Enhancers	Stomach Mucosa	stomach
7	chr14:78112000-78112400	Flanking Active TSS	K562	blood
8	chr14:78112200-78113200	Enhancers	Fetal Intestine Small	intestine

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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