Variant report

Variant	rs6540578
Chromosome Location	chr1:210236470-210236471
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:210229763..210232380-chr1:210235609..210237993,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11590161	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12401646	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12750599	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1338286	0.82[ASN][1000 genomes]
rs17318612	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17318744	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451696	0.93[EUR][1000 genomes]
rs2451697	0.93[EUR][1000 genomes]
rs2484030	0.92[EUR][1000 genomes]
rs2484031	0.92[EUR][1000 genomes]
rs2484032	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2484033	0.83[EUR][1000 genomes]
rs2484034	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485883	0.87[ASN][1000 genomes]
rs2485885	0.81[ASN][1000 genomes]
rs34704551	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34931444	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35256257	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4844954	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56131913	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61820396	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61820397	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61826848	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657016	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7543650	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv873140	chr1:210068117-210335644	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1821002	chr1:210108473-210291476	ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv873141	chr1:210228131-210296910	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv873142	chr1:210233610-210291121	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv873143	chr1:210233610-210296910	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210221400-210243200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr1:210223600-210245600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:210224400-210250000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:210235600-210238000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links