Variant report

Variant	rs4862580
Chromosome Location	chr4:186793887-186793888
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10001944	0.90[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs10002028	0.84[ASW][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];0.83[YRI][hapmap]
rs2310371	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs2603722	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.80[YRI][hapmap];0.90[ASN][1000 genomes]
rs2603724	0.85[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap]
rs2648107	0.84[CHB][hapmap]
rs2648111	0.85[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap]
rs4861686	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4862579	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4862585	0.81[CHD][hapmap]
rs4862587	0.81[CHD][hapmap]
rs6552931	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6552932	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7674855	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7675409	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9994907	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs9995677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[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	nsv1028146	chr4:186503899-187338335	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1023917	chr4:186533075-186997806	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537420	chr4:186533075-186997806	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv530178	chr4:186659940-187478310	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1015236	chr4:186696172-187004074	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1022661	chr4:186789827-187122464	Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv537422	chr4:186789827-187122464	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4862580	ODZ3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:186785600-186794800	Enhancers	Fetal Heart	heart
2	chr4:186787800-186795400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr4:186788000-186795400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr4:186789000-186795200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:186789000-186799600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:186790600-186795400	Weak transcription	Osteobl	bone
7	chr4:186791000-186795400	Weak transcription	Hela-S3	cervix
8	chr4:186791000-186799600	Weak transcription	Left Ventricle	heart
9	chr4:186791000-186799800	Weak transcription	Pancreas	Pancrea
10	chr4:186791400-186794000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:186791600-186795800	Weak transcription	HSMMtube	muscle
12	chr4:186791800-186802600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr4:186793000-186801000	Weak transcription	Spleen	Spleen
14	chr4:186793600-186795400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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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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