Variant report

Variant	rs58851315
Chromosome Location	chr7:66858719-66858720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11766952	0.84[AMR][1000 genomes]
rs11769345	0.84[AMR][1000 genomes]
rs11770922	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11773861	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4266531	0.84[AMR][1000 genomes]
rs66521840	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66669140	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66697341	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67794814	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs68034409	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs73137799	0.83[EUR][1000 genomes]
rs73140306	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv888330	chr7:66502171-66877880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv1031147	chr7:66811313-66922350	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1025049	chr7:66823977-66906930	Bivalent Enhancer Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv33523	chr7:66855435-66958898	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3478290	chr7:66858334-66859731	Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3515699	chr7:66858401-66859794	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv3515700	chr7:66858401-66859794	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3478291	chr7:66858425-66859649	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv10381	chr7:66858458-66859603	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs58851315	STAG3L4	cis	Skin Sun Exposed Lower leg	GTEx
rs58851315	RP11-166O4.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66857800-66859600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:66858000-66858800	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr7:66858200-66858800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr7:66858200-66859400	Enhancers	H1 Cell Line	embryonic stem cell
5	chr7:66858400-66858800	Flanking Active TSS	H9 Cell Line	embryonic stem cell
6	chr7:66858400-66859200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr7:66858400-66859200	Enhancers	Colon Smooth Muscle	Colon
8	chr7:66858400-66859200	Enhancers	Fetal Stomach	stomach
9	chr7:66858600-66858800	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr7:66858600-66858800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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Input of quick search could be:

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

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