Variant report

Variant	rs9654867
Chromosome Location	chr7:66829564-66829565
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11761674	0.98[ASN][1000 genomes]
rs11765153	0.88[AFR][1000 genomes]
rs11765818	0.88[AFR][1000 genomes]
rs1989425	0.86[AFR][1000 genomes]
rs2421293	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4718539	0.88[AFR][1000 genomes]
rs4718540	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6460340	0.88[AFR][1000 genomes]
rs6948506	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6978273	0.98[ASN][1000 genomes]
rs7796287	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1027702	chr7:66722103-66841913	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	nsv966840	chr7:66821082-66833953	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs9654867	FLJ13195	Cis_1M	lymphoblastoid	RTeQTL
rs9654867	STAG3L4	cis	Artery Tibial	GTEx
rs9654867	STAG3L4	cis	lung	GTEx
rs9654867	STAG3L4	cis	Adipose Subcutaneous	GTEx
rs9654867	STAG3L4	cis	Thyroid	GTEx
rs9654867	STAG3L4	cis	Esophagus Mucosa	GTEx
rs9654867	STAG3L4	cis	Whole Blood	GTEx
rs9654867	STAG3L4	cis	Esophagus Muscularis	GTEx
rs9654867	STAG3L4	cis	Nerve Tibial	GTEx
rs9654867	STAG3L4	cis	Skin Sun Exposed Lower leg	GTEx
rs9654867	STAG3L4	cis	Muscle Skeletal	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66810200-66830400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr7:66823000-66832200	Weak transcription	Brain Angular Gyrus	brain
3	chr7:66823200-66832000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr7:66824200-66830000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr7:66825200-66830600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr7:66825400-66829600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr7:66829000-66829600	Enhancers	Right Ventricle	heart
8	chr7:66829400-66829600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr7:66829400-66829800	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr7:66829400-66829800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr7:66829400-66829800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr7:66829400-66830000	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr7:66829400-66830000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr7:66829400-66830000	Enhancers	Placenta	Placenta

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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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