Variant report

Variant	rs4567413
Chromosome Location	chr11:47232184-47232185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47231611..47234324-chr11:47290633..47292856,2	K562	blood:
2	chr11:47230836..47232572-chr11:47289597..47292546,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000025434	Chromatin interaction
ENSG00000110514	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10466478	0.95[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.80[MKK][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10501319	0.84[GIH][hapmap]
rs1055447	0.80[CHD][hapmap];0.84[GIH][hapmap];0.84[ASN][1000 genomes]
rs1060573	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10742797	0.83[CHB][hapmap]
rs10769233	0.80[ASN][1000 genomes]
rs10769234	0.94[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10769239	0.84[ASN][1000 genomes]
rs10838644	0.81[GIH][hapmap]
rs10838652	0.81[GIH][hapmap]
rs10838654	0.83[ASN][1000 genomes]
rs10838659	0.88[ASN][1000 genomes]
rs10838660	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.88[ASN][1000 genomes]
rs10838662	0.84[GIH][hapmap]
rs10838664	0.80[CHD][hapmap];0.89[GIH][hapmap]
rs10838681	0.86[CHD][hapmap]
rs11039074	0.94[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs11039086	0.84[ASN][1000 genomes]
rs11039097	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.85[ASN][1000 genomes]
rs11039105	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11039107	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11039112	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11039119	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11039124	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11039134	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11600668	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11601798	0.80[CHB][hapmap]
rs12224096	0.95[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12291341	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417519	0.81[GIH][hapmap]
rs12574410	0.81[CHB][hapmap]
rs12796744	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.85[ASN][1000 genomes]
rs12807887	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1872896	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1965952	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1976142	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1976143	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2018527	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2029298	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2087215	0.84[GIH][hapmap]
rs2279439	0.89[GIH][hapmap]
rs4237547	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4319472	0.95[CEU][hapmap];0.85[ASN][1000 genomes]
rs4579897	0.81[ASN][1000 genomes]
rs4587689	0.81[GIH][hapmap]
rs4752952	0.81[ASN][1000 genomes]
rs4752957	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.85[ASN][1000 genomes]
rs4752962	0.95[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs4752963	0.86[ASN][1000 genomes]
rs4752967	0.95[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4752969	0.84[GIH][hapmap]
rs4752971	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57323109	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6485726	0.81[GIH][hapmap]
rs6485739	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.86[ASN][1000 genomes]
rs7103581	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.80[ASN][1000 genomes]
rs7108902	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs7111764	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7112854	0.80[GIH][hapmap]
rs7119952	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7121418	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7124648	0.81[GIH][hapmap]
rs7125807	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs7126005	0.81[GIH][hapmap]
rs7128650	0.81[GIH][hapmap]
rs7130006	0.80[CHD][hapmap];0.86[GIH][hapmap]
rs747650	0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7479189	0.95[CEU][hapmap];0.81[ASN][1000 genomes]
rs7931260	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs7937101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7937410	0.80[CHD][hapmap];0.89[GIH][hapmap]
rs7937950	0.83[ASN][1000 genomes]
rs7940240	0.80[CHD][hapmap];0.89[GIH][hapmap]
rs7942473	0.85[ASN][1000 genomes]
rs7945315	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs7946709	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.83[ASN][1000 genomes]
rs7950753	0.81[GIH][hapmap]
rs9633886	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4567413	NUP160	cis	cerebellum	SCAN
rs4567413	C11orf49	cis	parietal	SCAN
rs4567413	DDB2	cis	Skin Sun Exposed Lower leg	GTEx
rs4567413	ACP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47226400-47235800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:47226600-47234600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:47227200-47235600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:47231000-47232400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr11:47231200-47232400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:47231400-47232400	Enhancers	NHEK	skin
7	chr11:47231600-47232400	Weak transcription	HepG2	liver
8	chr11:47231600-47235200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr11:47232000-47235800	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links