Variant report

Variant	rs2839013
Chromosome Location	chr21:47248981-47248982
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47248821..47250626-chr21:47254393..47257357,2	MCF-7	breast:
2	chr21:47242037..47244390-chr21:47248096..47249777,2	MCF-7	breast:
3	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

Variant related genes	Relation type
ENSG00000205424	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1014446	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10854472	0.93[ASN][1000 genomes]
rs11089024	0.92[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs11089027	0.81[EUR][1000 genomes]
rs12481867	0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12481913	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12481970	0.91[ASN][1000 genomes]
rs12481977	0.93[ASN][1000 genomes]
rs12482010	0.91[ASN][1000 genomes]
rs12482094	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12482377	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12482750	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12482853	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1467758	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs17351419	0.93[ASN][1000 genomes]
rs17351433	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2065334	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2183595	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2183596	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2838973	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2838974	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2838976	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2838982	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2838989	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2838991	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2838992	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2838993	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2838994	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2838998	0.80[ASN][1000 genomes]
rs2838999	0.82[ASN][1000 genomes]
rs2839000	0.82[ASN][1000 genomes]
rs2839001	0.82[ASN][1000 genomes]
rs2839002	0.82[ASN][1000 genomes]
rs2839003	0.87[ASN][1000 genomes]
rs2839004	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2839005	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2839009	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2839014	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2839026	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2839029	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2839032	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3367	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs35781238	0.85[ASN][1000 genomes]
rs3788208	0.89[ASN][1000 genomes]
rs3788209	0.93[ASN][1000 genomes]
rs3788211	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3788215	0.90[ASN][1000 genomes]
rs3788216	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3788220	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3788224	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3788227	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3920695	0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs4434082	0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs4818801	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4818802	0.93[ASN][1000 genomes]
rs4818803	0.93[ASN][1000 genomes]
rs4818805	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4819151	0.82[ASN][1000 genomes]
rs4819152	0.82[ASN][1000 genomes]
rs4819154	0.94[ASN][1000 genomes]
rs4819155	0.93[ASN][1000 genomes]
rs4819156	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4819157	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs55780126	0.87[ASN][1000 genomes]
rs55856400	0.93[ASN][1000 genomes]
rs55875620	0.87[ASN][1000 genomes]
rs55912352	0.93[ASN][1000 genomes]
rs55927540	0.96[ASN][1000 genomes]
rs56036552	0.80[ASN][1000 genomes]
rs56256701	0.81[ASN][1000 genomes]
rs57688476	0.88[ASN][1000 genomes]
rs58952758	0.82[ASN][1000 genomes]
rs59785950	0.82[ASN][1000 genomes]
rs61063225	0.90[ASN][1000 genomes]
rs61276251	0.88[ASN][1000 genomes]
rs62211883	0.93[ASN][1000 genomes]
rs62211885	0.93[ASN][1000 genomes]
rs62211886	0.93[ASN][1000 genomes]
rs62211895	0.93[ASN][1000 genomes]
rs62211925	0.93[ASN][1000 genomes]
rs62211926	0.93[ASN][1000 genomes]
rs62214592	0.82[ASN][1000 genomes]
rs62214596	0.82[ASN][1000 genomes]
rs62214597	0.82[ASN][1000 genomes]
rs62214599	0.82[ASN][1000 genomes]
rs62214604	0.87[ASN][1000 genomes]
rs62214608	0.89[ASN][1000 genomes]
rs66523344	0.93[ASN][1000 genomes]
rs66991496	0.82[ASN][1000 genomes]
rs67055992	0.93[ASN][1000 genomes]
rs67878041	0.93[ASN][1000 genomes]
rs7280173	0.93[ASN][1000 genomes]
rs8127369	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs8127428	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs882668	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs882669	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs914241	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs9306139	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs9637208	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs964975	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9977908	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9978740	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9983770	0.93[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2839013	PCBP3	cis	cerebellum	SCAN
rs2839013	COL18A1	cis	parietal	SCAN
rs2839013	FTCD	cis	cerebellum	SCAN
rs2839013	COL6A1	cis	cerebellum	SCAN

Chromatin state (count:16 , 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	chr21:47247000-47257600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr21:47247200-47249400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr21:47247200-47257000	Weak transcription	Spleen	Spleen
13	chr21:47247600-47249200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr21:47248000-47257200	Weak transcription	Primary T cells from cord blood	blood
15	chr21:47248600-47253800	Enhancers	Adipose Nuclei	Adipose
16	chr21:47248800-47250000	Strong transcription	Fetal Thymus	thymus

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