Variant report

Variant	rs914243
Chromosome Location	chr21:47155316-47155317
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	chr21:47155045..47157882-chr21:47165789..47168073,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL6A1-3	chr21:47155306-47155343	NONHSAT082981
2	lnc-COL6A1-3	chr21:47155306-47155343	NONHSAT082983
3	lnc-COL6A1-3	chr21:47155306-47155343	NONHSAT082985

Variant related genes	Relation type
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11089022	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs11702443	0.95[CHB][hapmap]
rs11702478	1.00[CHB][hapmap]
rs11702850	0.93[ASN][1000 genomes]
rs11911839	0.93[ASN][1000 genomes]
rs12373907	0.90[ASN][1000 genomes]
rs12627257	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs1556335	0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2075885	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs2150452	0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs2297293	0.92[ASN][1000 genomes]
rs2330245	0.93[ASN][1000 genomes]
rs2838972	0.90[ASN][1000 genomes]
rs2838984	0.95[ASN][1000 genomes]
rs2839006	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs2839015	0.95[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs2839027	0.95[CHB][hapmap]
rs2839028	0.95[CHB][hapmap]
rs2839034	0.95[CHB][hapmap];0.83[CHD][hapmap]
rs34582204	0.82[ASN][1000 genomes]
rs34627227	0.81[ASN][1000 genomes]
rs35930369	0.81[ASN][1000 genomes]
rs3788219	0.95[CHB][hapmap]
rs4819145	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4819146	0.95[ASN][1000 genomes]
rs7278438	0.93[ASN][1000 genomes]
rs7281669	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs743352	1.00[CHB][hapmap]
rs744507	0.84[ASN][1000 genomes]
rs8128153	0.84[ASN][1000 genomes]
rs8128559	0.82[ASN][1000 genomes]
rs8129304	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs8134872	0.95[CHB][hapmap];0.88[CHD][hapmap]
rs9306138	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs9306141	0.95[ASN][1000 genomes]
rs9977795	0.95[ASN][1000 genomes]
rs9978181	0.95[ASN][1000 genomes]
rs9979633	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1063957	chr21:47090475-47168291	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
9	nsv1062702	chr21:47095762-47169369	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
10	nsv544493	chr21:47095762-47169369	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs914243	COL6A1	cis	parietal	SCAN
rs914243	COL6A1	cis	Artery Tibial	GTEx
rs914243	COL6A1	cis	cerebellum	SCAN
rs914243	SLC37A1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47135600-47165000	Weak transcription	Primary T cells from cord blood	blood
2	chr21:47144200-47167600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr21:47144600-47157600	Weak transcription	Right Atrium	heart
4	chr21:47145400-47156200	Weak transcription	Brain Substantia Nigra	brain
5	chr21:47146600-47159600	Weak transcription	Spleen	Spleen
6	chr21:47146600-47160000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr21:47151200-47155400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr21:47151800-47164800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr21:47152600-47157600	Strong transcription	Fetal Thymus	thymus
10	chr21:47152600-47160400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr21:47153200-47165400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr21:47154000-47156600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr21:47154400-47158000	Strong transcription	Thymus	Thymus
14	chr21:47154400-47160000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr21:47154800-47156800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr21:47155200-47156200	Enhancers	Fetal Heart	heart
17	chr21:47155200-47158600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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