Variant report

Variant	rs10012612
Chromosome Location	chr4:74516528-74516529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10023093	0.95[EUR][1000 genomes]
rs10032975	0.95[EUR][1000 genomes]
rs11733985	0.96[EUR][1000 genomes]
rs11735458	0.95[EUR][1000 genomes]
rs1247602	0.87[AMR][1000 genomes]
rs1247604	0.87[AMR][1000 genomes]
rs1247676	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1247678	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12641279	0.82[CHB][hapmap]
rs12648230	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs12650864	0.96[EUR][1000 genomes]
rs2091588	0.94[EUR][1000 genomes]
rs28560041	0.98[EUR][1000 genomes]
rs28829089	0.86[AMR][1000 genomes]
rs6833774	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7655717	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7665555	0.97[EUR][1000 genomes]
rs998234	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1008104	chr4:74468434-74621952	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1012198	chr4:74487793-74621952	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv537139	chr4:74487793-74621952	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10012612	CXCL3	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74514000-74519200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr4:74514200-74517000	Enhancers	Fetal Thymus	thymus
3	chr4:74515400-74517400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:74515400-74519400	Enhancers	Thymus	Thymus
5	chr4:74516000-74517000	Weak transcription	Placenta	Placenta
6	chr4:74516400-74517600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:74516400-74517600	Enhancers	HMEC	breast
8	chr4:74516400-74517800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:74516400-74517800	Enhancers	NHEK	skin
10	chr4:74516400-74525000	Weak transcription	Stomach Mucosa	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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