Variant report

Variant	rs3747006
Chromosome Location	chr21:47721661-47721662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47719443..47722298-chr21:47727196..47729251,2	MCF-7	breast:
2	chr21:47718509..47724261-chr21:47732959..47738534,9	K562	blood:
3	chr21:47647161..47649856-chr21:47719709..47722524,2	MCF-7	breast:
4	chr21:47700722..47725192-chr21:47732201..47746452,77	K562	blood:
5	chr21:47705928..47708356-chr21:47720533..47726820,5	K562	blood:

Variant related genes	Relation type
ENSG00000215424	Chromatin interaction
ENSG00000160298	Chromatin interaction
ENSG00000160294	Chromatin interaction
ENSG00000160285	Chromatin interaction
ENSG00000182362	Chromatin interaction
ENSG00000160299	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11089056	0.99[ASN][1000 genomes]
rs11089061	0.96[ASN][1000 genomes]
rs11700398	0.93[ASN][1000 genomes]
rs11700435	0.92[ASN][1000 genomes]
rs11700519	0.96[ASN][1000 genomes]
rs11701707	0.97[ASN][1000 genomes]
rs11701725	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12626184	0.94[ASN][1000 genomes]
rs12627400	0.88[ASN][1000 genomes]
rs13047780	0.98[ASN][1000 genomes]
rs13049522	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1556336	0.99[ASN][1000 genomes]
rs1556337	0.99[ASN][1000 genomes]
rs1888539	0.87[ASN][1000 genomes]
rs1974171	0.99[ASN][1000 genomes]
rs2276258	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2839202	0.94[ASN][1000 genomes]
rs2839203	0.94[ASN][1000 genomes]
rs2839204	0.93[ASN][1000 genomes]
rs2839206	0.96[ASN][1000 genomes]
rs2839207	0.97[ASN][1000 genomes]
rs3747007	0.99[ASN][1000 genomes]
rs4818834	0.97[ASN][1000 genomes]
rs4818835	0.98[ASN][1000 genomes]
rs4819236	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4989912	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4989913	0.81[ASN][1000 genomes]
rs61446584	0.96[ASN][1000 genomes]
rs62224180	0.82[ASN][1000 genomes]
rs6518287	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7277438	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8651	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs914249	0.96[ASN][1000 genomes]
rs914252	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 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	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
21	nsv587975	chr21:47661235-47830843	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	n/a
22	nsv432159	chr21:47673247-47854392	Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	n/a
23	nsv527355	chr21:47678774-47863025	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	n/a
24	nsv914135	chr21:47681041-47762374	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	n/a
25	nsv914136	chr21:47681041-47900994	Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	n/a
26	nsv1064588	chr21:47700051-47788823	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	n/a
27	nsv544496	chr21:47700051-47788823	Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	n/a
28	nsv914137	chr21:47700498-47862624	Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	n/a
29	nsv914138	chr21:47700498-47866227	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	n/a
30	nsv914139	chr21:47706737-47786494	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
31	nsv914140	chr21:47712185-47866227	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	n/a
32	nsv914141	chr21:47712412-47757419	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	n/a
33	nsv587980	chr21:47715296-47722530	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs3747006	C21orf57	cis	multi-tissue	Pritchard
rs3747006	YBEY	cis	Skin Sun Exposed Lower leg	GTEx
rs3747006	YBEY	cis	Nerve Tibial	GTEx
rs3747006	YBEY	cis	Whole Blood	GTEx
rs3747006	YBEY	cis	Artery Tibial	GTEx
rs3747006	YBEY	cis	Thyroid	GTEx
rs3747006	YBEY	cis	Muscle Skeletal	GTEx
rs3747006	AP001469.9	cis	Thyroid	GTEx
rs3747006	YBEY	cis	Adipose Subcutaneous	GTEx
rs3747006	C21orf57	Cis_1M	lymphoblastoid	RTeQTL
rs3747006	YBEY	cis	lung	GTEx
rs3747006	YBEY	cis	Esophagus Mucosa	GTEx
rs3747006	YBEY	cis	Stomach	GTEx
rs3747006	YBEY	cis	Esophagus Muscularis	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47710000-47727600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr21:47716200-47727200	Weak transcription	HSMMtube	muscle
3	chr21:47716400-47727000	Weak transcription	HSMM	muscle
4	chr21:47716600-47724400	Weak transcription	K562	blood
5	chr21:47716800-47738600	Weak transcription	HepG2	liver
6	chr21:47717400-47723200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr21:47717800-47739600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr21:47718000-47729200	Weak transcription	Aorta	Aorta
9	chr21:47718000-47736000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr21:47718200-47721800	Weak transcription	Esophagus	oesophagus
11	chr21:47718200-47721800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr21:47718200-47721800	Weak transcription	Ovary	ovary
13	chr21:47718200-47722000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr21:47718200-47722000	Weak transcription	Placenta	Placenta
15	chr21:47718200-47722600	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr21:47718200-47724400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr21:47718200-47724400	Weak transcription	Brain Angular Gyrus	brain
18	chr21:47718200-47724400	Weak transcription	NH-A	brain
19	chr21:47718200-47724600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr21:47718200-47724600	Weak transcription	Primary B cells from cord blood	blood
21	chr21:47718200-47724600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr21:47718200-47724600	Weak transcription	Brain Substantia Nigra	brain
23	chr21:47718200-47724600	Weak transcription	Fetal Kidney	kidney
24	chr21:47718200-47724600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr21:47718200-47724600	Weak transcription	NHDF-Ad	bronchial
26	chr21:47718200-47726800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr21:47718200-47731600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr21:47718200-47737400	Weak transcription	Fetal Heart	heart
29	chr21:47718200-47737800	Weak transcription	Colonic Mucosa	Colon
30	chr21:47718200-47740800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr21:47718200-47742000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr21:47718200-47742200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr21:47718400-47721800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr21:47718400-47722800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr21:47718400-47724200	Weak transcription	Fetal Intestine Large	intestine
36	chr21:47718400-47724400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr21:47718400-47724400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr21:47718400-47724400	Weak transcription	Adipose Nuclei	Adipose
39	chr21:47718400-47724400	Weak transcription	Liver	Liver
40	chr21:47718400-47724400	Weak transcription	Fetal Brain Female	brain
41	chr21:47718400-47724400	Weak transcription	HMEC	breast
42	chr21:47718400-47724400	Weak transcription	HUVEC	blood vessel
43	chr21:47718400-47726600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr21:47718400-47727400	Weak transcription	Pancreas	Pancrea
45	chr21:47718400-47728400	Weak transcription	Primary T cells from cord blood	blood
46	chr21:47718400-47737600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr21:47718400-47737600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr21:47718400-47737600	Weak transcription	Right Ventricle	heart
49	chr21:47718400-47737800	Weak transcription	Left Ventricle	heart
50	chr21:47718400-47740200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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