Variant report

Variant	rs56134439
Chromosome Location	chr21:47732271-47732272
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:47731336-47732769	K562	blood:	n/a	n/a
2	POLR2A	chr21:47731939-47732436	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:47721939..47724799-chr21:47732004..47733970,2	MCF-7	breast:
2	chr21:47700722..47725192-chr21:47732201..47746452,77	K562	blood:
3	chr21:47551026..47553790-chr21:47731962..47734784,2	K562	blood:
4	chr21:47705682..47708439-chr21:47732061..47733790,2	MCF-7	breast:

Variant related genes	Relation type
C21orf58	TF binding region
ENSG00000182362	Chromatin interaction
ENSG00000160294	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11089060	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2015083	0.96[EUR][1000 genomes]
rs2839210	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2839211	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55696586	0.84[ASN][1000 genomes]
rs56107738	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs56134439	SPATC1L	cis	Skin Sun Exposed Lower leg	GTEx
rs56134439	SPATC1L	cis	Thyroid	GTEx
rs56134439	C21orf57	Cis_1M	lymphoblastoid	RTeQTL
rs56134439	SPATC1L	cis	Muscle Skeletal	GTEx
rs56134439	SPATC1L	cis	Artery Tibial	GTEx
rs56134439	YBEY	cis	Muscle Skeletal	GTEx
rs56134439	SPATC1L	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47716800-47738600	Weak transcription	HepG2	liver
2	chr21:47717800-47739600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr21:47718000-47736000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr21:47718200-47737400	Weak transcription	Fetal Heart	heart
5	chr21:47718200-47737800	Weak transcription	Colonic Mucosa	Colon
6	chr21:47718200-47740800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr21:47718200-47742000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr21:47718200-47742200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr21:47718400-47737600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr21:47718400-47737600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr21:47718400-47737600	Weak transcription	Right Ventricle	heart
12	chr21:47718400-47737800	Weak transcription	Left Ventricle	heart
13	chr21:47718400-47740200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr21:47718400-47740600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr21:47718400-47741600	Weak transcription	Fetal Brain Male	brain
16	chr21:47718400-47742200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr21:47718400-47742200	Weak transcription	Right Atrium	heart
18	chr21:47718600-47738000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr21:47719000-47738200	Strong transcription	Fetal Stomach	stomach
20	chr21:47719000-47738800	Strong transcription	Dnd41	blood
21	chr21:47719200-47738800	Strong transcription	Fetal Thymus	thymus
22	chr21:47719600-47739400	Strong transcription	Thymus	Thymus
23	chr21:47719600-47740200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr21:47720200-47740600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr21:47721400-47733400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr21:47722400-47734400	Weak transcription	Esophagus	oesophagus
27	chr21:47722400-47734400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr21:47722400-47742000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr21:47722400-47742200	Weak transcription	Gastric	stomach
30	chr21:47722600-47733200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr21:47722600-47733400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr21:47722600-47736600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr21:47724400-47739600	Strong transcription	Fetal Muscle Leg	muscle
34	chr21:47724800-47734800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr21:47725000-47733200	Weak transcription	Fetal Brain Female	brain
36	chr21:47725000-47740400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr21:47725000-47742200	Weak transcription	Adipose Nuclei	Adipose
38	chr21:47725000-47742200	Weak transcription	Brain Hippocampus Middle	brain
39	chr21:47725000-47742200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr21:47725000-47742400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr21:47725200-47733200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr21:47725200-47733200	Weak transcription	Fetal Intestine Large	intestine
43	chr21:47725200-47734400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr21:47725200-47735400	Weak transcription	NHLF	lung
45	chr21:47725200-47737000	Weak transcription	Spleen	Spleen
46	chr21:47725200-47737200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr21:47725200-47737400	Weak transcription	GM12878-XiMat	blood
48	chr21:47725200-47737800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr21:47725200-47738000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr21:47725200-47740000	Weak transcription	Hela-S3	cervix

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