Variant report

Variant	rs16979001
Chromosome Location	chr21:47654301-47654302
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47646929..47655402-chr21:47657205..47667464,13	MCF-7	breast:
2	chr21:47653995..47656077-chr21:47743565..47746155,2	K562	blood:
3	chr12:6579433..6580135-chr21:47653785..47654319,2	NB4	blood:
4	chr21:47653573..47654422-chr21:47666524..47667070,2	K562	blood:
5	chr21:47653008..47655194-chr21:47704386..47706163,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160299	Chromatin interaction
ENSG00000139190	Chromatin interaction
ENSG00000160294	Chromatin interaction
ENSG00000160298	Chromatin interaction
ENSG00000228137	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs16979006	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16979014	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17176170	0.97[EUR][1000 genomes]
rs17176352	1.00[EUR][1000 genomes]
rs17182573	0.94[EUR][1000 genomes]
rs17182643	0.97[EUR][1000 genomes]
rs17183017	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17183081	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17183262	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17183283	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28560443	0.81[EUR][1000 genomes]
rs28801979	1.00[CEU][hapmap]
rs35785446	0.86[EUR][1000 genomes]
rs60322177	1.00[EUR][1000 genomes]
rs73386515	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73386563	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73386596	1.00[EUR][1000 genomes]
rs8127105	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8134875	1.00[CEU][hapmap]
rs9975914	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
8	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
9	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
10	nsv1059118	chr21:47398331-48090457	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
11	nsv544494	chr21:47398331-48090457	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
12	nsv934264	chr21:47401083-48090317	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
13	nsv1060978	chr21:47488073-47833640	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	n/a
14	nsv519904	chr21:47583506-47881309	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
15	nsv948761	chr21:47587940-48069930	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	n/a
16	nsv1055239	chr21:47591378-48090317	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
17	nsv544495	chr21:47591378-48090317	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
18	nsv933354	chr21:47609029-47851401	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a
19	nsv949706	chr21:47625544-48069930	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
20	nsv914134	chr21:47632995-47712185	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	n/a
21	nsv529496	chr21:47634193-48090317	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16979001	C21orf56	cis	lymphoblastoid	seeQTL
rs16979001	C21orf56	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47649800-47654400	Weak transcription	Aorta	Aorta
2	chr21:47649800-47654400	Weak transcription	Colonic Mucosa	Colon
3	chr21:47649800-47654400	Weak transcription	Right Ventricle	heart
4	chr21:47649800-47701600	Weak transcription	Right Atrium	heart
5	chr21:47650000-47654400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr21:47650000-47658600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr21:47650000-47658600	Weak transcription	Small Intestine	intestine
8	chr21:47650000-47705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr21:47650200-47654800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr21:47650200-47667000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr21:47650400-47654400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr21:47650400-47654400	Weak transcription	Stomach Mucosa	stomach
13	chr21:47650400-47658800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr21:47650600-47654600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr21:47650600-47656800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr21:47650600-47669800	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr21:47650800-47656600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr21:47650800-47701000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr21:47650800-47701400	Strong transcription	Fetal Muscle Leg	muscle
20	chr21:47650800-47701600	Strong transcription	Fetal Stomach	stomach
21	chr21:47651000-47656800	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr21:47651000-47656800	Strong transcription	NHEK	skin
23	chr21:47651000-47703200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr21:47651200-47656800	Strong transcription	A549	lung
25	chr21:47651200-47657200	Strong transcription	HMEC	breast
26	chr21:47651200-47657400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr21:47651200-47657400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr21:47651200-47701400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr21:47651400-47656800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr21:47651400-47657000	Strong transcription	NH-A	brain
31	chr21:47651600-47657800	Strong transcription	Fetal Intestine Large	intestine
32	chr21:47651600-47670400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr21:47651600-47673000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr21:47651600-47679000	Strong transcription	HSMM	muscle
35	chr21:47651600-47703000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr21:47651600-47703200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr21:47651800-47654600	Weak transcription	HepG2	liver
38	chr21:47651800-47655800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr21:47651800-47656600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr21:47651800-47656800	Strong transcription	Primary T cells from cord blood	blood
41	chr21:47651800-47656800	Strong transcription	Primary hematopoietic stem cells	blood
42	chr21:47651800-47657000	Strong transcription	NHDF-Ad	bronchial
43	chr21:47651800-47657200	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr21:47651800-47657600	Strong transcription	Ovary	ovary
45	chr21:47651800-47657600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr21:47651800-47657800	Strong transcription	Brain Hippocampus Middle	brain
47	chr21:47651800-47657800	Strong transcription	Fetal Muscle Trunk	muscle
48	chr21:47651800-47657800	Strong transcription	Left Ventricle	heart
49	chr21:47651800-47666800	Strong transcription	Fetal Lung	lung
50	chr21:47651800-47681000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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