Variant report

Variant	rs958648
Chromosome Location	chr8:11103895-11103896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10098488	0.81[CEU][hapmap]
rs11777002	0.81[EUR][1000 genomes]
rs12541649	0.90[ASN][1000 genomes]
rs1347410	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2572408	0.88[EUR][1000 genomes]
rs2572417	0.92[CEU][hapmap];0.84[TSI][hapmap]
rs2572418	0.92[CEU][hapmap]
rs2572430	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2572431	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2736371	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2736372	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2736375	0.85[EUR][1000 genomes]
rs6601573	0.81[TSI][hapmap]
rs6601577	0.82[EUR][1000 genomes]
rs7824557	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9286062	0.84[TSI][hapmap]

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	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv1815171	chr8:10940039-11128712	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv831233	chr8:11046854-11234384	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1022525	chr8:11066191-11309356	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv539474	chr8:11066191-11309356	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv890353	chr8:11097804-11110503	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs958648	DEFB134	cis	cerebellum	SCAN
rs958648	TDH	cis	cerebellum	SCAN
rs958648	TDH	cis	parietal	SCAN
rs958648	BLK	cis	lymphoblastoid	seeQTL
rs958648	C8orf13	cis	multi-tissue	Pritchard
rs958648	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs958648	BLK	Cis_1M	lymphoblastoid	RTeQTL
rs958648	CTSB	cis	cerebellum	SCAN
rs958648	FLJ10661	cis	cerebellum	SCAN
rs958648	C8orf13	Cis_1M	lymphoblastoid	RTeQTL
rs958648	C8orf48	cis	cerebellum	SCAN
rs958648	CLDN23	cis	multi-tissue	Pritchard

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11101200-11116000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:11102000-11105600	Weak transcription	GM12878-XiMat	blood
3	chr8:11102400-11108000	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr8:11103600-11104400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr8:11103800-11104400	Enhancers	HMEC	breast

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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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