Variant report

Variant	rs4668394
Chromosome Location	chr2:172454319-172454320
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10185715	0.80[ASN][1000 genomes]
rs10211146	0.89[YRI][hapmap];0.92[ASN][1000 genomes]
rs10221787	0.93[ASN][1000 genomes]
rs10432471	0.84[ASN][1000 genomes]
rs10930485	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11680862	0.98[ASN][1000 genomes]
rs11680897	0.98[ASN][1000 genomes]
rs11683752	0.94[ASN][1000 genomes]
rs11683762	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.96[ASN][1000 genomes]
rs11686621	0.98[ASN][1000 genomes]
rs11689452	0.89[ASN][1000 genomes]
rs11689637	0.82[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.96[ASN][1000 genomes]
rs12472229	0.93[ASN][1000 genomes]
rs12476299	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12996145	0.82[ASW][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs13002792	0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs13024519	0.94[CHB][hapmap];0.84[JPT][hapmap];0.96[ASN][1000 genomes]
rs13025303	0.96[ASN][1000 genomes]
rs1473995	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs1807872	0.95[ASN][1000 genomes]
rs1996268	0.89[ASN][1000 genomes]
rs2884028	0.83[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs4667691	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668391	0.92[ASN][1000 genomes]
rs4668392	0.92[ASN][1000 genomes]
rs4668393	0.96[ASN][1000 genomes]
rs6704691	0.86[ASN][1000 genomes]
rs6711201	0.92[ASN][1000 genomes]
rs6745725	0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs6747775	0.86[ASN][1000 genomes]
rs7575168	0.81[ASN][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	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv997638	chr2:172442205-172560406	Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
3	nsv525490	chr2:172453700-172454933	Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4668394	ZAK	cis	parietal	SCAN
rs4668394	CYBRD1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172452400-172454800	Weak transcription	Adipose Nuclei	Adipose
2	chr2:172452800-172455600	Weak transcription	HMEC	breast
3	chr2:172453000-172454800	Weak transcription	NHLF	lung
4	chr2:172453000-172455200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:172453000-172455600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:172453000-172455600	Weak transcription	A549	lung
7	chr2:172453000-172455800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:172453200-172455000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:172453200-172455600	Weak transcription	NHDF-Ad	bronchial
10	chr2:172453200-172455800	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links