Variant report

Variant	rs7794479
Chromosome Location	chr7:66843080-66843081
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2421293	0.81[EUR][1000 genomes]
rs4718540	0.83[EUR][1000 genomes]
rs6948506	0.83[EUR][1000 genomes]
rs7788614	0.81[AFR][1000 genomes]
rs7796287	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1031048	chr7:66722103-66844039	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats 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	32 gene(s)	inside rSNPs	diseases
5	nsv1031560	chr7:66805244-66846663	Enhancers Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1022779	chr7:66805244-66849392	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	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
8	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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7794479	STAG3L4	cis	Adipose Subcutaneous	GTEx
rs7794479	STAG3L4	cis	Artery Aorta	GTEx
rs7794479	RP11-166O4.5	cis	Thyroid	GTEx
rs7794479	STAG3L4	cis	Artery Tibial	GTEx
rs7794479	FLJ13195	Cis_1M	lymphoblastoid	RTeQTL
rs7794479	STAG3L4	cis	Whole Blood	GTEx
rs7794479	STAG3L4	cis	Esophagus Muscularis	GTEx
rs7794479	STAG3L4	cis	lung	GTEx
rs7794479	STAG3L4	cis	Skin Sun Exposed Lower leg	GTEx
rs7794479	STAG3L4	cis	Thyroid	GTEx
rs7794479	STAG3L4	cis	Nerve Tibial	GTEx
rs7794479	STAG3L4	cis	Muscle Skeletal	GTEx
rs7794479	STAG3L4	cis	Esophagus Mucosa	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66840800-66843600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:66842800-66843600	Enhancers	Fetal Brain Female	brain
3	chr7:66842800-66844000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr7:66842800-66844000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr7:66842800-66844200	Enhancers	Fetal Muscle Leg	muscle
6	chr7:66843000-66843600	Enhancers	Fetal Brain Male	brain
7	chr7:66843000-66843800	Enhancers	Brain Hippocampus Middle	brain
8	chr7:66843000-66843800	Enhancers	Spleen	Spleen
9	chr7:66843000-66844000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:66843000-66844000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr7:66843000-66844000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr7:66843000-66847200	Enhancers	Fetal Stomach	stomach

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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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