Variant report

Variant	rs6518251
Chromosome Location	chr21:47017128-47017129
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47016711..47019230-chr21:47061555..47064496,2	K562	blood:
2	chr21:47013893..47017287-chr21:47018957..47021547,4	MCF-7	breast:
3	chr21:46974617..46977834-chr21:47015409..47018050,3	K562	blood:
4	chr21:46975609..46976596-chr21:47015982..47017270,9	K562	blood:
5	chr21:46959711..46962395-chr21:47016786..47019577,2	MCF-7	breast:
6	chr21:46969440..46972420-chr21:47016292..47018421,2	K562	blood:
7	chr21:46975645..46976567-chr21:47016257..47017243,9	MCF-7	breast:
8	chr21:46974460..46976647-chr21:47016051..47017288,20	MCF-7	breast:
9	chr21:46974308..46977530-chr21:47014075..47018729,9	MCF-7	breast:
10	chr21:47016056..47017268-chr21:47188399..47189168,3	MCF-7	breast:
11	chr21:47016307..47019935-chr21:47020452..47024014,6	K562	blood:
12	chr21:46974154..46977331-chr21:47015385..47017284,4	MCF-7	breast:
13	chr21:46974494..46977601-chr21:47013740..47018269,6	K562	blood:

No data

No data

No data

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11089016	0.85[ASN][1000 genomes]
rs13047047	0.90[ASN][1000 genomes]
rs13050787	0.91[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13052853	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1556333	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2150445	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2838963	0.87[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2838965	0.89[ASN][1000 genomes]
rs36063916	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6518252	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7283542	0.87[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs8128868	0.87[ASN][1000 genomes]
rs8129128	0.85[ASN][1000 genomes]
rs8129873	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs879612	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs914238	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1057807	chr21:46656346-47077374	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
3	esv2762114	chr21:46680202-47067744	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
5	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
6	nsv516407	chr21:46830873-47040656	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
7	nsv914048	chr21:46839904-47032872	Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
8	esv1822272	chr21:46848326-47038855	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
9	nsv914066	chr21:46912386-47053962	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv834112	chr21:46922151-47048253	Strong transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv459309	chr21:46932328-47021784	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv587862	chr21:46932328-47021784	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
13	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
14	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
15	nsv914077	chr21:46998548-47091361	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6518251	PFKL	cis	cerebellum	SCAN
rs6518251	C15orf54	trans	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47012200-47021800	Weak transcription	Right Atrium	heart
2	chr21:47015000-47017400	Enhancers	Fetal Thymus	thymus
3	chr21:47015800-47019200	Strong transcription	K562	blood
4	chr21:47016200-47017200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr21:47016200-47017400	Enhancers	Thymus	Thymus
6	chr21:47016400-47017200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
7	chr21:47016400-47017200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr21:47016400-47017200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr21:47016400-47017200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr21:47016600-47017200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr21:47016600-47017200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr21:47016600-47017200	Enhancers	Ovary	ovary
13	chr21:47016600-47017200	Enhancers	Dnd41	blood
14	chr21:47016600-47021000	ZNF genes & repeats	GM12878-XiMat	blood

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links