Variant report

Variant	rs1729987
Chromosome Location	chr3:98317836-98317837
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1675524	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1729992	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs1729993	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs828600	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528056	chr3:98101101-98317836	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv520503	chr3:98102801-98317836	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv834775	chr3:98170059-98367552	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv997484	chr3:98284283-98371420	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1000357	chr3:98284283-98381473	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv524042	chr3:98317836-98436188	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1729987	CPOX	cis	cerebellum	SCAN
rs1729987	EPHA6	cis	cerebellum	SCAN
rs1729987	ST3GAL6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98313000-98321400	Enhancers	Liver	Liver
2	chr3:98313200-98321200	Weak transcription	Fetal Thymus	thymus
3	chr3:98313200-98322600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:98315200-98321000	Enhancers	HepG2	liver
5	chr3:98315800-98319400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr3:98316000-98319600	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr3:98316800-98318000	Enhancers	GM12878-XiMat	blood
8	chr3:98317000-98318000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr3:98317200-98321000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:98317200-98322400	Weak transcription	K562	blood
11	chr3:98317400-98322200	Weak transcription	Thymus	Thymus
12	chr3:98317800-98322400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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