Variant report

Variant	rs9980967
Chromosome Location	chr21:47033905-47033906
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2838967	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28801527	0.87[EUR][1000 genomes]
rs4369959	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819136	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55654342	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs725930	0.87[CEU][hapmap]
rs7280089	0.87[CEU][hapmap]
rs73230568	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230569	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8133338	0.87[CEU][hapmap]
rs9798668	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9976523	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9977594	0.87[CEU][hapmap]
rs9984042	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1057807	chr21:46656346-47077374	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
3	esv2762114	chr21:46680202-47067744	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv516407	chr21:46830873-47040656	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
7	esv1822272	chr21:46848326-47038855	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
8	nsv914066	chr21:46912386-47053962	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv834112	chr21:46922151-47048253	Strong transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv914077	chr21:46998548-47091361	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
13	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
14	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9980967	COL6A1	cis	parietal	SCAN
rs9980967	AGPAT3	cis	cerebellum	SCAN
rs9980967	PCBP3	cis	cerebellum	SCAN
rs9980967	KRTAP10-5	cis	parietal	SCAN
rs9980967	FAM3B	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47022000-47039000	Weak transcription	Right Atrium	heart
2	chr21:47027200-47037600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr21:47032400-47035200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr21:47033200-47034200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
5	chr21:47033200-47034800	Enhancers	Fetal Thymus	thymus
6	chr21:47033200-47034800	Enhancers	Thymus	Thymus
7	chr21:47033200-47035000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr21:47033400-47034000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr21:47033400-47034800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr21:47033400-47034800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr21:47033400-47035000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr21:47033400-47035000	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr21:47033400-47035000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr21:47033600-47034000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr21:47033600-47034000	Enhancers	Primary T cells from cord blood	blood
16	chr21:47033600-47034000	Bivalent Enhancer	HSMMtube	muscle
17	chr21:47033600-47034200	Bivalent Enhancer	Adipose Nuclei	Adipose
18	chr21:47033600-47035000	Enhancers	Dnd41	blood
19	chr21:47033800-47034000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr21:47033800-47034000	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr21:47033800-47034000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr21:47033800-47034000	Bivalent Enhancer	Fetal Lung	lung
23	chr21:47033800-47034000	Enhancers	GM12878-XiMat	blood
24	chr21:47033800-47034000	Bivalent Enhancer	K562	blood
25	chr21:47033800-47034800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr21:47033800-47035000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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