Variant report

Variant	rs7859900
Chromosome Location	chr9:22529933-22529934
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10511702	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511703	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1125421	0.86[EUR][1000 genomes]
rs13288577	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13301478	0.85[EUR][1000 genomes]
rs1499553	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17694996	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17836077	0.85[EUR][1000 genomes]
rs1999124	0.85[EUR][1000 genomes]
rs34813395	0.86[EUR][1000 genomes]
rs35100496	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35308147	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4269626	0.84[EUR][1000 genomes]
rs72697736	0.84[EUR][1000 genomes]
rs7466514	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1029289	chr9:22193167-23023688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv869121	chr9:22382290-23232146	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv2761508	chr9:22400968-22819938	Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1016983	chr9:22412948-22672062	Bivalent/Poised TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1027227	chr9:22416348-22666768	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv540088	chr9:22416348-22666768	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv533941	chr9:22416549-23232146	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv1814118	chr9:22496582-22537010	Enhancers Weak transcription ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
11	esv1821031	chr9:22496582-22537010	Enhancers Weak transcription ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
12	nsv892758	chr9:22502851-22596808	Weak transcription Enhancers Strong transcription ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
13	nsv892759	chr9:22502851-22705094	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1033655	chr9:22509328-22565473	ZNF genes & repeats Weak transcription Enhancers Strong transcription	lncRNA	n/a	inside rSNPs	diseases
15	nsv1024068	chr9:22512564-22555567	Weak transcription Enhancers ZNF genes & repeats Strong transcription	lncRNA	n/a	inside rSNPs	diseases
16	nsv540089	chr9:22512564-22555567	Enhancers Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
17	nsv1026370	chr9:22512564-22610935	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases
18	nsv540090	chr9:22512564-22610935	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases
19	nsv466298	chr9:22513927-22562121	Enhancers ZNF genes & repeats Weak transcription Strong transcription	lncRNA	n/a	inside rSNPs	diseases
20	nsv613784	chr9:22513927-22562121	Enhancers Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7859900	ADAMTSL1	cis	parietal	SCAN
rs7859900	SCARNA8	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22528800-22530000	Enhancers	Skeletal Muscle Male	skeletal muscle
2	chr9:22528800-22531000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:22529400-22530000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr9:22529400-22530200	Enhancers	Adipose Nuclei	Adipose
5	chr9:22529600-22530600	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr9:22529800-22530600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:22529800-22531000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links