Variant report

Variant	rs2839034
Chromosome Location	chr21:47296585-47296586
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47290619..47293353-chr21:47296443..47298286,2	K562	blood:
2	chr21:47295466..47298745-chr21:47300328..47303080,5	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11089022	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs11089023	0.92[ASN][1000 genomes]
rs11702443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11702478	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11702552	0.95[ASN][1000 genomes]
rs12627257	0.91[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1783075	0.91[ASW][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap]
rs2075885	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2150452	0.91[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs2839006	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2839007	0.84[ASN][1000 genomes]
rs2839012	0.91[ASN][1000 genomes]
rs2839015	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]
rs2839016	0.90[ASN][1000 genomes]
rs2839027	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2839028	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2839042	0.84[GIH][hapmap];0.88[MEX][hapmap]
rs2839044	0.80[CHD][hapmap]
rs2839045	0.86[GIH][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap]
rs373617	0.84[GIH][hapmap];0.84[MEX][hapmap]
rs3788219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs381083	0.84[GIH][hapmap];0.84[MEX][hapmap]
rs431609	0.91[ASW][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap]
rs4819145	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4819162	0.84[JPT][hapmap]
rs61496907	0.92[ASN][1000 genomes]
rs7276396	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7281669	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs741955	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs743352	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8129118	0.84[ASN][1000 genomes]
rs8129304	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs8132054	0.80[CHD][hapmap]
rs8134872	0.91[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs914243	0.95[CHB][hapmap];0.83[CHD][hapmap]
rs9306138	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9979633	0.91[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 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
15	nsv914080	chr21:47265786-47311686	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS 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	2 gene(s)	inside rSNPs	n/a
16	nsv914081	chr21:47265786-47320805	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
17	nsv914082	chr21:47265786-47338007	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
18	nsv914083	chr21:47265786-47453954	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
19	nsv914084	chr21:47288453-47326666	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
20	esv14817	chr21:47293464-47303825	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2839034	COL6A1	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47266800-47300600	Weak transcription	Right Atrium	heart
2	chr21:47273800-47299200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr21:47293000-47299000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr21:47294400-47297000	Bivalent Enhancer	Fetal Stomach	stomach
5	chr21:47294400-47298400	Enhancers	Placenta	Placenta
6	chr21:47294600-47296800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr21:47294600-47297000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr21:47294800-47297000	Enhancers	NHLF	lung
9	chr21:47294800-47299200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr21:47295000-47297800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr21:47295000-47298000	Enhancers	NH-A	brain
12	chr21:47295000-47298200	Enhancers	NHDF-Ad	bronchial
13	chr21:47295000-47298400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr21:47295000-47298600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr21:47295000-47298600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr21:47295000-47298800	Enhancers	HSMMtube	muscle
17	chr21:47295200-47297200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr21:47295200-47297400	Enhancers	Fetal Lung	lung
19	chr21:47295400-47296800	Enhancers	Right Ventricle	heart
20	chr21:47295400-47297000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr21:47295400-47297000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr21:47295400-47299800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr21:47295400-47299800	Weak transcription	Fetal Thymus	thymus
24	chr21:47295600-47297200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr21:47295600-47297200	Enhancers	NHEK	skin
26	chr21:47295600-47298600	Enhancers	HSMM	muscle
27	chr21:47295600-47300000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr21:47295600-47300200	Weak transcription	Thymus	Thymus
29	chr21:47295600-47309200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr21:47295800-47296600	Enhancers	Spleen	Spleen
31	chr21:47295800-47296800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr21:47295800-47297200	Enhancers	Fetal Kidney	kidney
33	chr21:47295800-47297600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr21:47295800-47297600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr21:47295800-47298200	Enhancers	Muscle Satellite Cultured Cells	--
36	chr21:47295800-47298200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr21:47295800-47298400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr21:47296000-47296800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr21:47296000-47296800	Enhancers	Brain Germinal Matrix	brain
40	chr21:47296000-47297200	Enhancers	Fetal Heart	heart
41	chr21:47296000-47297800	Weak transcription	Osteobl	bone
42	chr21:47296000-47298400	Enhancers	Fetal Muscle Leg	muscle
43	chr21:47296200-47297200	Enhancers	Fetal Brain Female	brain
44	chr21:47296200-47298000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr21:47296400-47296600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr21:47296400-47296600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr21:47296400-47296600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
48	chr21:47296400-47296800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr21:47296400-47297000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr21:47296400-47297000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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