Variant report

Variant	rs12644965
Chromosome Location	chr4:74731526-74731527
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10020344	0.83[ASN][1000 genomes]
rs10518118	0.83[ASN][1000 genomes]
rs12643330	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1429638	0.87[CHD][hapmap];0.91[MKK][hapmap];0.83[ASN][1000 genomes]
rs4422395	0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs4694644	0.83[ASN][1000 genomes]
rs4694649	0.81[ASN][1000 genomes]
rs56366267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs625837	0.84[ASN][1000 genomes]
rs7438101	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv432612	chr4:74723372-74774372	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12644965	CXCL6	cis	parietal	SCAN
rs12644965	SEPT11	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74719400-74733600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:74726000-74734200	Weak transcription	HSMM	muscle
3	chr4:74726200-74733600	Weak transcription	NHDF-Ad	bronchial
4	chr4:74726400-74733800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:74728600-74734200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:74728800-74734000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:74729200-74733600	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr4:74730000-74731800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:74730000-74732600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:74730200-74732000	Weak transcription	HMEC	breast
11	chr4:74730400-74731600	Weak transcription	NHEK	skin
12	chr4:74731000-74731600	Enhancers	Muscle Satellite Cultured Cells	--
13	chr4:74731200-74732800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:74731400-74734200	Weak transcription	Monocytes-CD14+_RO01746	blood

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