Variant report

Variant	rs2424635
Chromosome Location	chr20:24717085-24717086
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2245957	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2424629	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2424630	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2424631	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2424632	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2424633	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2424637	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34709197	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs36062686	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4239747	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4239748	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4239749	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4815302	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs60577833	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs910237	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs910238	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs910239	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs910240	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1061412	chr20:24629468-24887869	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv544216	chr20:24629468-24887869	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1061281	chr20:24711635-24815107	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv544217	chr20:24711635-24815107	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv912825	chr20:24715544-24813345	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Bipolar disorder and schizophrenia	20889312	GWAS catalog

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24710000-24718000	Weak transcription	Spleen	Spleen
2	chr20:24714000-24718400	Weak transcription	Thymus	Thymus
3	chr20:24715000-24717400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr20:24715000-24718400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr20:24715200-24719000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr20:24715400-24718000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr20:24716200-24717600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr20:24716200-24717600	Enhancers	Fetal Stomach	stomach
9	chr20:24716200-24717800	Weak transcription	Placenta	Placenta
10	chr20:24716200-24723800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr20:24716400-24717600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr20:24716400-24717600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr20:24716400-24717600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr20:24716600-24717800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr20:24716800-24717200	Enhancers	Fetal Thymus	thymus
16	chr20:24716800-24717200	Enhancers	NH-A	brain
17	chr20:24716800-24717800	Enhancers	Fetal Lung	lung
18	chr20:24717000-24719800	Weak transcription	Colon Smooth Muscle	Colon
19	chr20:24717000-24719800	Weak transcription	Stomach Smooth Muscle	stomach

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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

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