Variant report

Variant	rs681824
Chromosome Location	chr1:228139489-228139490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
WNT9A	TF binding region
ENSG00000143740	Chromatin interaction
ENSG00000143816	Chromatin interaction
ENSG00000081692	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11584326	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1418422	0.90[EUR][1000 genomes]
rs1636193	0.92[EUR][1000 genomes]
rs1636194	0.93[EUR][1000 genomes]
rs1636196	0.81[ASN][1000 genomes]
rs1774754	0.92[EUR][1000 genomes]
rs2262292	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2485254	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796055	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587000	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601050	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs638877	0.96[EUR][1000 genomes]
rs640440	0.93[EUR][1000 genomes]
rs652141	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs662658	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680148	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs708109	0.84[ASN][1000 genomes]
rs708110	0.84[ASN][1000 genomes]
rs849900	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
7	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
9	nsv873251	chr1:228051234-228160911	Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs681824	OBSCN	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228136800-228139600	Weak transcription	Esophagus	oesophagus
2	chr1:228136800-228141000	Weak transcription	Ovary	ovary
3	chr1:228136800-228141000	Weak transcription	NHDF-Ad	bronchial
4	chr1:228137000-228141000	Weak transcription	HSMMtube	muscle
5	chr1:228137200-228140600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:228137200-228141000	Weak transcription	HSMM	muscle
7	chr1:228138000-228141000	Weak transcription	Fetal Lung	lung
8	chr1:228138400-228139600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:228138400-228139800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:228138400-228140000	Weak transcription	Spleen	Spleen
11	chr1:228138400-228140200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:228139400-228142000	Bivalent Enhancer	Fetal Stomach	stomach

Quick Search:

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

what's new

Quick links