Variant report

Variant	rs7528731
Chromosome Location	chr1:59404995-59404996
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11207323	0.91[MEX][hapmap]
rs11207325	0.91[CEU][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes]
rs11207332	0.87[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12117564	0.91[MEX][hapmap]
rs12122077	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12404569	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1536159	0.91[CEU][hapmap]
rs2038863	0.81[ASN][1000 genomes]
rs2057596	0.83[CEU][hapmap]
rs2716127	0.88[ASN][1000 genomes]
rs2764914	0.81[CHB][hapmap]
rs2953373	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3015312	0.81[CHB][hapmap]
rs4912382	0.85[CHB][hapmap]
rs6658104	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs6661505	0.91[CEU][hapmap];0.91[MEX][hapmap]
rs6664131	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs6677752	1.00[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];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74078024	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005354	chr1:59283572-59535812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv829959	chr1:59340330-59503085	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv546316	chr1:59368947-59457815	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7528731	OMA1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59389000-59407000	Weak transcription	Spleen	Spleen
2	chr1:59393600-59406800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:59399000-59405800	Weak transcription	Pancreas	Pancrea
4	chr1:59399000-59406800	Weak transcription	Esophagus	oesophagus
5	chr1:59399000-59407000	Weak transcription	Lung	lung
6	chr1:59399200-59407200	Weak transcription	Colonic Mucosa	Colon
7	chr1:59399200-59409400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:59399400-59405200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:59399400-59405800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:59401600-59407000	Weak transcription	Gastric	stomach
11	chr1:59402600-59408400	Weak transcription	A549	lung
12	chr1:59403200-59408000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:59403200-59408200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:59403200-59408200	Weak transcription	NHEK	skin
15	chr1:59403400-59408000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:59403400-59408200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:59403400-59408200	Weak transcription	HMEC	breast
18	chr1:59404400-59407200	Enhancers	Primary T cells fromperipheralblood	blood

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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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