Variant report

Variant	rs7422809
Chromosome Location	chr2:56176031-56176032
allele	C/T
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	CEBPB	chr2:56175367-56176048	IMR90	lung:	n/a	chr2:56175877-56175888 chr2:56175833-56175845 chr2:56175875-56175886
2	CEBPB	chr2:56174729-56176073	Hela-S3	cervix:	n/a	chr2:56175877-56175888 chr2:56175833-56175845 chr2:56175875-56175886

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:56174984..56177810-chr2:56181564..56184235,2	K562	blood:
2	chr2:56169478..56172187-chr2:56174953..56177671,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272180	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10185077	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10192259	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11125611	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12472832	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13431149	0.90[ASN][1000 genomes]
rs1432560	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1432561	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1432563	0.91[ASN][1000 genomes]
rs1432564	0.90[ASN][1000 genomes]
rs1465685	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1583266	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1583267	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1897478	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2278366	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2868984	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34552760	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3972318	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4258837	0.92[CHB][hapmap]
rs4453721	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4635565	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4672080	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4672081	0.91[ASN][1000 genomes]
rs4672082	0.91[ASN][1000 genomes]
rs55805406	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545531	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6704991	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6721145	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6724998	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6733881	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6733889	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6747490	0.90[ASN][1000 genomes]
rs724539	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs724540	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7561395	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7561417	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7564964	0.91[ASN][1000 genomes]
rs981037	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv874161	chr2:56154316-56203798	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56171000-56176400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:56171000-56185000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:56171200-56176400	Weak transcription	NHEK	skin
4	chr2:56174600-56176400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:56174800-56176400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:56174800-56176400	Enhancers	Osteobl	bone
7	chr2:56174800-56177000	Enhancers	Hela-S3	cervix
8	chr2:56175000-56177000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:56175000-56177000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:56175200-56176400	Weak transcription	Fetal Kidney	kidney
11	chr2:56175600-56181400	Weak transcription	HUVEC	blood vessel
12	chr2:56175800-56176400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr2:56176000-56181400	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links