Variant report

Variant	rs2839015
Chromosome Location	chr21:47250239-47250240
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	chr21:47248821..47250626-chr21:47254393..47257357,2	MCF-7	breast:
2	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: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11089022	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11089023	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11702443	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11702478	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs11702552	0.90[ASN][1000 genomes]
rs12627257	0.90[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1547240	0.80[CHD][hapmap]
rs1556335	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1783075	0.90[ASW][hapmap];0.80[CHD][hapmap];1.00[LWK][hapmap]
rs2075885	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2150452	0.90[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap]
rs2839006	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2839007	0.93[ASN][1000 genomes]
rs2839012	0.93[ASN][1000 genomes]
rs2839016	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2839027	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2839028	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2839034	0.82[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2839042	0.80[CHD][hapmap];0.80[GIH][hapmap]
rs2839044	0.80[CHD][hapmap]
rs2839045	0.80[CHD][hapmap];0.82[GIH][hapmap]
rs373617	0.80[CHD][hapmap];0.80[GIH][hapmap];0.90[LWK][hapmap]
rs3788219	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs381083	0.80[CHD][hapmap];0.80[GIH][hapmap]
rs431609	0.90[ASW][hapmap];0.80[CHD][hapmap];1.00[LWK][hapmap]
rs4819145	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4819150	0.87[ASN][1000 genomes]
rs4819168	0.80[CHD][hapmap]
rs61496907	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7276396	0.91[ASN][1000 genomes]
rs7281669	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs741955	0.92[ASN][1000 genomes]
rs743352	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs8129118	0.94[ASN][1000 genomes]
rs8129304	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs8132054	0.80[CHD][hapmap]
rs8134872	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.82[TSI][hapmap]
rs914243	0.95[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs9306138	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9979633	0.90[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2839015	COL6A1	cis	cerebellum	SCAN

Chromatin state (count:24 , 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	chr21:47241600-47257400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr21:47241800-47257600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr21:47247000-47257600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr21:47247200-47257000	Weak transcription	Spleen	Spleen
9	chr21:47248000-47257200	Weak transcription	Primary T cells from cord blood	blood
10	chr21:47248600-47253800	Enhancers	Adipose Nuclei	Adipose
11	chr21:47249000-47251200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr21:47249200-47251000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr21:47249200-47251000	Bivalent Enhancer	Fetal Stomach	stomach
14	chr21:47249200-47251200	Enhancers	Fetal Muscle Leg	muscle
15	chr21:47249200-47253400	Weak transcription	Thymus	Thymus
16	chr21:47249400-47250600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr21:47249400-47251000	Enhancers	Placenta	Placenta
18	chr21:47249800-47250400	Enhancers	Duodenum Mucosa	Duodenum
19	chr21:47249800-47256000	Weak transcription	Fetal Lung	lung
20	chr21:47250000-47250800	Weak transcription	Fetal Thymus	thymus
21	chr21:47250000-47252400	Weak transcription	Right Ventricle	heart
22	chr21:47250200-47250600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr21:47250200-47250600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr21:47250200-47251000	Enhancers	HUES6 Cell Line	embryonic stem cell

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