Variant report

Variant	rs13050787
Chromosome Location	chr21:47016967-47016968
allele	A/G
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:17)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:47016711..47019230-chr21:47061555..47064496,2	K562	blood:
2	chr21:46974706..46975271-chr21:47016568..47017114,2	MCF-7	breast:
3	chr21:47013893..47017287-chr21:47018957..47021547,4	MCF-7	breast:
4	chr21:46974617..46977834-chr21:47015409..47018050,3	K562	blood:
5	chr21:46975609..46976596-chr21:47015982..47017270,9	K562	blood:
6	chr21:47014325..47017105-chr21:47027718..47030231,2	MCF-7	breast:
7	chr21:46897754..46898338-chr21:47016482..47017033,2	MCF-7	breast:
8	chr21:46959711..46962395-chr21:47016786..47019577,2	MCF-7	breast:
9	chr21:46969440..46972420-chr21:47016292..47018421,2	K562	blood:
10	chr21:46975645..46976567-chr21:47016257..47017243,9	MCF-7	breast:
11	chr21:47010941..47014214-chr21:47014784..47017085,3	MCF-7	breast:
12	chr21:46974460..46976647-chr21:47016051..47017288,20	MCF-7	breast:
13	chr21:46974308..46977530-chr21:47014075..47018729,9	MCF-7	breast:
14	chr21:47016056..47017268-chr21:47188399..47189168,3	MCF-7	breast:
15	chr21:47016307..47019935-chr21:47020452..47024014,6	K562	blood:
16	chr21:46974154..46977331-chr21:47015385..47017284,4	MCF-7	breast:
17	chr21:46974494..46977601-chr21:47013740..47018269,6	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PCBP3-1	chr21:47016305-47017005	XLOC_013985

No data

Variant related genes	Relation type
ENSG00000183570	Chromatin interaction
ENSG00000173638	Chromatin interaction
ENSG00000233922	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11089016	0.93[ASN][1000 genomes]
rs13047047	0.99[ASN][1000 genomes]
rs13047348	0.85[ASN][1000 genomes]
rs13052853	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1556333	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2150446	0.80[ASN][1000 genomes]
rs2838963	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2838965	0.97[ASN][1000 genomes]
rs36063916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6518251	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]
rs6518252	0.87[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7283542	0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs8128868	0.95[ASN][1000 genomes]
rs8129128	0.93[ASN][1000 genomes]
rs8129873	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs879612	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs914238	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.96[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13050787	C15orf54	trans	parietal	SCAN

Chromatin state (count:23 , 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	chr21:47016400-47017000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
7	chr21:47016400-47017000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr21:47016400-47017000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr21:47016400-47017000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr21:47016400-47017000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr21:47016400-47017200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr21:47016400-47017200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr21:47016400-47017200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr21:47016400-47017200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr21:47016600-47017000	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr21:47016600-47017000	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr21:47016600-47017000	Enhancers	Duodenum Mucosa	Duodenum
18	chr21:47016600-47017000	Enhancers	Stomach Mucosa	stomach
19	chr21:47016600-47017200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr21:47016600-47017200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr21:47016600-47017200	Enhancers	Ovary	ovary
22	chr21:47016600-47017200	Enhancers	Dnd41	blood
23	chr21:47016600-47021000	ZNF genes & repeats	GM12878-XiMat	blood

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