Variant report

Variant	rs55927540
Chromosome Location	chr21:47247979-47247980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47246654..47249179-chr21:47249623..47252084,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC19A1-3	chr21:47247875-47251155	ENSG00000205424.1
2	lnc-SLC19A1-3	chr21:47247755-47251155	NONHSAT082996

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1014446	0.93[ASN][1000 genomes]
rs10854472	0.96[ASN][1000 genomes]
rs11089024	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12481867	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12481913	0.94[ASN][1000 genomes]
rs12481970	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12481977	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12482010	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12482094	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12482377	0.96[ASN][1000 genomes]
rs12482853	0.90[ASN][1000 genomes]
rs17351419	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17351433	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2065334	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838997	0.81[ASN][1000 genomes]
rs2838998	0.83[ASN][1000 genomes]
rs2838999	0.86[ASN][1000 genomes]
rs2839000	0.86[ASN][1000 genomes]
rs2839001	0.86[ASN][1000 genomes]
rs2839002	0.86[ASN][1000 genomes]
rs2839003	0.90[ASN][1000 genomes]
rs2839004	0.90[ASN][1000 genomes]
rs2839005	0.90[ASN][1000 genomes]
rs2839009	0.88[ASN][1000 genomes]
rs2839013	0.96[ASN][1000 genomes]
rs2839014	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839026	0.96[ASN][1000 genomes]
rs2839029	0.93[ASN][1000 genomes]
rs2839032	0.93[ASN][1000 genomes]
rs35781238	0.81[ASN][1000 genomes]
rs3788208	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3788209	0.96[ASN][1000 genomes]
rs3788211	0.96[ASN][1000 genomes]
rs3788215	0.94[ASN][1000 genomes]
rs3788216	0.96[ASN][1000 genomes]
rs3788220	0.96[ASN][1000 genomes]
rs3788224	0.93[ASN][1000 genomes]
rs3788227	0.96[ASN][1000 genomes]
rs4818801	0.86[ASN][1000 genomes]
rs4818802	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4818803	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4818805	0.93[ASN][1000 genomes]
rs4819151	0.86[ASN][1000 genomes]
rs4819152	0.86[ASN][1000 genomes]
rs4819154	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4819155	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4819156	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4819157	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55780126	0.90[ASN][1000 genomes]
rs55856400	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55875620	0.90[ASN][1000 genomes]
rs55912352	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs55996718	0.87[AFR][1000 genomes]
rs56036552	0.83[ASN][1000 genomes]
rs56256701	0.85[ASN][1000 genomes]
rs56347571	0.81[ASN][1000 genomes]
rs57688476	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58952758	0.86[ASN][1000 genomes]
rs59785950	0.86[ASN][1000 genomes]
rs61063225	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61276251	0.91[ASN][1000 genomes]
rs62211883	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62211885	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62211886	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62211895	0.96[ASN][1000 genomes]
rs62211925	0.96[ASN][1000 genomes]
rs62211926	0.96[ASN][1000 genomes]
rs62214592	0.86[ASN][1000 genomes]
rs62214596	0.86[ASN][1000 genomes]
rs62214597	0.86[ASN][1000 genomes]
rs62214599	0.86[ASN][1000 genomes]
rs62214604	0.90[ASN][1000 genomes]
rs62214608	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66523344	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66991496	0.86[ASN][1000 genomes]
rs67055992	0.96[ASN][1000 genomes]
rs67878041	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7280173	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8127428	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs882668	0.90[ASN][1000 genomes]
rs882669	0.93[ASN][1000 genomes]
rs9637208	0.96[ASN][1000 genomes]
rs964975	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9983770	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
3	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
4	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
5	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
6	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
8	nsv428043	chr21:47179244-47471971	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a
9	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
10	nsv914078	chr21:47218744-47311686	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
11	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
12	esv2756755	chr21:47243032-47319768	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
13	esv2758821	chr21:47243032-47319768	Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
14	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55927540	PCBP3	cis	lung	GTEx
rs55927540	PCBP3	cis	Muscle Skeletal	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47217800-47260400	Weak transcription	Right Atrium	heart
2	chr21:47240600-47256600	Weak transcription	Dnd41	blood
3	chr21:47241000-47251800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr21:47241000-47255400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr21:47241200-47250200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr21:47241400-47249600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr21:47241600-47257400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr21:47241800-47257600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr21:47244800-47249200	Strong transcription	Thymus	Thymus
10	chr21:47246400-47248200	Enhancers	Fetal Thymus	thymus
11	chr21:47246800-47248200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr21:47246800-47248400	Enhancers	Primary B cells from peripheral blood	blood
13	chr21:47247000-47248000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr21:47247000-47248000	Enhancers	GM12878-XiMat	blood
15	chr21:47247000-47248400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr21:47247000-47248400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr21:47247000-47257600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr21:47247200-47248000	Enhancers	Primary T cells from cord blood	blood
19	chr21:47247200-47248200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr21:47247200-47248400	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr21:47247200-47249400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr21:47247200-47257000	Weak transcription	Spleen	Spleen
23	chr21:47247400-47248200	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr21:47247600-47248000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr21:47247600-47248200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr21:47247600-47248400	Enhancers	Primary T cells fromperipheralblood	blood
27	chr21:47247600-47249200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr21:47247800-47248200	Enhancers	Primary T helper naive cells from peripheral blood	blood

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