Variant report

Variant	rs9976523
Chromosome Location	chr21:47032395-47032396
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	chr21:47023058..47028814-chr21:47029340..47033815,7	MCF-7	breast:
2	chr21:47030755..47033887-chr21:47035586..47039018,4	K562	blood:

Extended variants
information (count: 29 )
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	0.90[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	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230569	1.00[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]
rs9977594	0.87[CEU][hapmap]
rs9980967	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9984042	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv914048	chr21:46839904-47032872	Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
rs9976523	AGPAT3	cis	cerebellum	SCAN
rs9976523	COL6A1	cis	parietal	SCAN
rs9976523	FAM3B	cis	cerebellum	SCAN
rs9976523	KRTAP10-5	cis	parietal	SCAN
rs9976523	PCBP3	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47022000-47039000	Weak transcription	Right Atrium	heart
2	chr21:47027200-47033400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr21:47027200-47037600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr21:47028600-47033400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr21:47028600-47033400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr21:47028800-47033400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr21:47028800-47033400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr21:47028800-47033800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr21:47030000-47033200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr21:47030800-47032600	Strong transcription	Thymus	Thymus
11	chr21:47031200-47032800	ZNF genes & repeats	Fetal Thymus	thymus
12	chr21:47031400-47032600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr21:47031800-47032400	Bivalent Enhancer	Fetal Brain Female	brain
14	chr21:47031800-47032400	Flanking Active TSS	HSMMtube	muscle
15	chr21:47031800-47032600	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr21:47031800-47032600	Enhancers	Rectal Smooth Muscle	rectum
17	chr21:47031800-47032800	Enhancers	HMEC	breast
18	chr21:47031800-47032800	Enhancers	NHLF	lung
19	chr21:47032000-47032400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr21:47032000-47032400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr21:47032000-47032400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
22	chr21:47032000-47032400	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr21:47032000-47032400	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
24	chr21:47032000-47032400	Bivalent Enhancer	Brain Substantia Nigra	brain
25	chr21:47032000-47032400	Flanking Active TSS	HSMM	muscle
26	chr21:47032000-47032800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr21:47032000-47032800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr21:47032000-47032800	Bivalent Enhancer	NHEK	skin
29	chr21:47032000-47033000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr21:47032000-47033600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr21:47032200-47032400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr21:47032200-47032400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr21:47032200-47032400	Active TSS	A549	lung
34	chr21:47032200-47032400	Flanking Active TSS	NH-A	brain
35	chr21:47032200-47032400	Bivalent/Poised TSS	Osteobl	bone
36	chr21:47032200-47032600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr21:47032200-47032800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr21:47032200-47032800	Bivalent Enhancer	Stomach Smooth Muscle	stomach

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