Variant report

Variant	rs56125920
Chromosome Location	chr6:45613314-45613315
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	ZNF143	chr6:45613233-45613433	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:45611643..45613817-chr6:45619919..45622769,2	K562	blood:
2	chr6:45606805..45609759-chr6:45609969..45613635,3	K562	blood:

Variant related genes	Relation type
RNU6-515P	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1889595	0.85[EUR][1000 genomes]
rs56383386	0.83[EUR][1000 genomes]
rs57847751	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58033063	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58899441	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59086975	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60021834	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60089305	0.83[ASN][1000 genomes]
rs60499694	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60653179	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60902957	0.83[ASN][1000 genomes]
rs61046945	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61433014	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61735894	0.96[EUR][1000 genomes]
rs61735906	0.96[EUR][1000 genomes]
rs6906753	0.81[EUR][1000 genomes]
rs6932213	0.85[EUR][1000 genomes]
rs73444596	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73446524	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73735415	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73735416	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73738524	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7755911	0.85[EUR][1000 genomes]
rs976319	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[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	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv427755	chr6:45474631-45627025	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45608400-45615200	Weak transcription	NH-A	brain
2	chr6:45608600-45617800	Weak transcription	Osteobl	bone
3	chr6:45608800-45614400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:45608800-45616800	Weak transcription	NHDF-Ad	bronchial
5	chr6:45609000-45616000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:45611200-45617800	Weak transcription	NHLF	lung
7	chr6:45611400-45614400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:45611400-45615000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:45611400-45618600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:45612000-45613400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr6:45612200-45613400	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr6:45612200-45615200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:45612400-45613400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr6:45612400-45623600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:45612600-45613400	Enhancers	GM12878-XiMat	blood
16	chr6:45612800-45613400	Enhancers	Primary B cells from peripheral blood	blood
17	chr6:45613000-45614200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:45613200-45613400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:45613200-45614200	Weak transcription	HSMM	muscle
20	chr6:45613200-45615000	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links