Variant report

Variant	rs1976142
Chromosome Location	chr11:47225694-47225695
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr11:47225588-47225735	K562	blood:	n/a	n/a
2	CTCF	chr11:47225595-47225835	K562	blood:	n/a	n/a
3	CTCF	chr11:47225640-47225790	Hela-S3	cervix:	n/a	n/a
4	GATA3	chr11:47225687-47226588	MCF-7	breast:	n/a	chr11:47226059-47226076 chr11:47226068-47226077
5	CTCF	chr11:47225620-47225770	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:47223065..47227984-chr11:47233675..47238356,6	MCF-7	breast:
2	chr11:47203683..47208496-chr11:47223862..47228000,5	MCF-7	breast:
3	chr11:47219819..47221860-chr11:47224771..47227015,2	MCF-7	breast:
4	chr11:47214523..47217185-chr11:47223816..47226023,3	MCF-7	breast:

Variant related genes	Relation type
RN7SL772P	TF binding region
ENSG00000134574	Chromatin interaction
ENSG00000165912	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10466478	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1055447	0.83[ASN][1000 genomes]
rs1060573	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10769239	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10838654	0.81[ASN][1000 genomes]
rs10838659	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10838660	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11039086	0.83[ASN][1000 genomes]
rs11039097	0.83[ASN][1000 genomes]
rs11039105	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11039107	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11039112	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11039119	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11039124	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11039134	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11600668	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12224096	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12291341	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12796744	0.83[ASN][1000 genomes]
rs12807887	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1872896	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1965952	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1976143	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2018527	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2029298	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4237547	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4319472	0.83[ASN][1000 genomes]
rs4567413	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4752957	0.83[ASN][1000 genomes]
rs4752962	0.85[ASN][1000 genomes]
rs4752963	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4752967	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4752971	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57323109	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6485739	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7111764	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7119952	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7121418	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs747650	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7937101	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7937950	0.81[ASN][1000 genomes]
rs7942473	0.83[ASN][1000 genomes]
rs7945315	0.83[ASN][1000 genomes]
rs7946709	0.81[ASN][1000 genomes]
rs9633886	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1976142	DDB2	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47210200-47226000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:47223000-47226000	Weak transcription	HepG2	liver
3	chr11:47224400-47225800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr11:47224400-47230200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr11:47224600-47225800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:47225600-47226000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr11:47225600-47226000	Enhancers	Hela-S3	cervix
8	chr11:47225600-47226200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr11:47225600-47226200	Enhancers	NHEK	skin
10	chr11:47225600-47226800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:47225600-47227200	Enhancers	HMEC	breast
12	chr11:47225600-47227200	Enhancers	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links