Variant report

Variant	rs13050837
Chromosome Location	chr21:40817356-40817357
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	MAX	chr21:40817210-40818167	Hela-S3	cervix:	n/a	chr21:40817927-40817936
2	MYC	chr21:40817337-40818462	NB4	blood:	n/a	chr21:40817927-40817936
3	POLR2A	chr21:40817220-40818107	NB4	blood:	n/a	n/a
4	E2F4	chr21:40817353-40818037	MCF10A-Er-Src	breast:	n/a	chr21:40817761-40817770 chr21:40817746-40817756
5	POLR2A	chr21:40817303-40818089	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr21:40817213-40818200	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr21:40817244-40818209	MCF-7	breast:	n/a	n/a
8	CCNT2	chr21:40817050-40818075	K562	blood:	n/a	n/a
9	MAZ	chr21:40817103-40818110	K562	blood:	n/a	chr21:40817927-40817936
10	GABPA	chr21:40817296-40818097	K562	blood:	n/a	chr21:40817760-40817774 chr21:40817760-40817769 chr21:40817762-40817771 chr21:40817757-40817771 chr21:40817760-40817771
11	MXI1	chr21:40817025-40818197	K562	blood:	n/a	n/a
12	NR2F2	chr21:40816977-40818203	MCF-7	breast:	n/a	n/a
13	POLR2A	chr21:40817248-40818167	Hela-S3	cervix:	n/a	n/a
14	HDAC2	chr21:40817313-40818095	H1-hESC	embryonic stem cell:	n/a	chr21:40817760-40817769
15	SIN3AK20	chr21:40816970-40818280	MCF-7	breast:	n/a	n/a
16	SMARCB1	chr21:40817251-40818077	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr21:40816598-40818147	IMR90	lung:	n/a	n/a
18	TAF1	chr21:40817301-40818159	H1-neurons	neurons:	n/a	n/a
19	EGR1	chr21:40817310-40818179	HCT-116	colon:	n/a	chr21:40817744-40817758 chr21:40817327-40817342 chr21:40817328-40817341 chr21:40817328-40817341 chr21:40817761-40817770
20	POLR2A	chr21:40817220-40818284	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr21:40817330-40818271	K562	blood:	n/a	chr21:40817777-40817790 chr21:40817736-40817749
22	MAX	chr21:40817183-40818176	MCF-7	breast:	n/a	chr21:40817927-40817936
23	POLR2A	chr21:40817324-40818135	PANC-1	pancreas:	n/a	n/a
24	MYC	chr21:40816901-40818552	K562	blood:	n/a	chr21:40817927-40817936
25	STAT1	chr21:40817272-40817435	GM12878	blood:	n/a	n/a
26	HCFC1	chr21:40817066-40818622	Hela-S3	cervix:	n/a	n/a
27	RCOR1	chr21:40817210-40818391	K562	blood:	n/a	n/a
28	CTCF	chr21:40817320-40817470	BE2_C	brain:	n/a	n/a
29	MXI1	chr21:40817305-40818185	GM12878	blood:	n/a	n/a
30	HDAC2	chr21:40817169-40818267	MCF-7	breast:	n/a	chr21:40817760-40817769 chr21:40818093-40818107 chr21:40818095-40818109 chr21:40818096-40818110 chr21:40818094-40818108
31	GATA2	chr21:40816678-40817858	SH-SY5Y	brain:	n/a	chr21:40817179-40817187
32	PML	chr21:40817233-40818099	MCF-7	breast:	n/a	n/a
33	MAZ	chr21:40816767-40818164	IMR90	lung:	n/a	chr21:40817927-40817936
34	TAF1	chr21:40817203-40818140	ECC-1	luminal epithelium:	n/a	n/a
35	ZNF143	chr21:40817043-40818372	K562	blood:	n/a	chr21:40817746-40817756
36	KAP1	chr21:40817329-40818192	HEK293	kidney:	n/a	n/a
37	MXI1	chr21:40817260-40818052	HepG2	liver:	n/a	n/a
38	SMARCC1	chr21:40816551-40818214	Hela-S3	cervix:	n/a	n/a
39	BHLHE40	chr21:40817326-40818111	K562	blood:	n/a	chr21:40817778-40817794
40	TAF1	chr21:40817226-40818114	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr21:40817325-40818229	MCF-7	breast:	n/a	n/a
42	POLR2A	chr21:40817326-40818130	A549	lung:	n/a	n/a
43	ELF1	chr21:40817237-40818042	K562	blood:	n/a	n/a
44	ZBTB7A	chr21:40817241-40818059	K562	blood:	n/a	n/a
45	ELF1	chr21:40817262-40818170	MCF-7	breast:	n/a	n/a
46	SIN3AK20	chr21:40817311-40817884	HepG2	liver:	n/a	n/a
47	ZMIZ1	chr21:40817306-40818467	K562	blood:	n/a	n/a
48	EGR1	chr21:40817139-40818131	K562	blood:	n/a	chr21:40817744-40817758 chr21:40817327-40817342 chr21:40817328-40817341 chr21:40817328-40817341 chr21:40817761-40817770
49	EP300	chr21:40817296-40818100	ECC-1	luminal epithelium:	n/a	chr21:40817786-40817802 chr21:40817739-40817755
50	E2F6	chr21:40817277-40818161	A549	lung:	n/a	chr21:40817761-40817770 chr21:40817746-40817756 chr21:40817922-40817933

No.	Distal block	Cell Line	Cell type
1	chr21:40552682..40557091-chr21:40814575..40819975,14	K562	blood:
2	chr21:40570372..40572709-chr21:40816957..40818525,2	MCF-7	breast:
3	chr21:40719238..40723494-chr21:40813785..40819496,7	MCF-7	breast:
4	chr21:40750443..40753981-chr21:40814998..40818130,3	MCF-7	breast:
5	chr21:40808402..40815127-chr21:40815513..40821149,12	K562	blood:
6	chr21:40552682..40557546-chr21:40815502..40820280,12	K562	blood:
7	chr21:40684209..40686276-chr21:40817224..40819799,4	MCF-7	breast:
8	chr21:40758092..40760884-chr21:40816362..40818206,3	K562	blood:
9	chr21:40684107..40685647-chr21:40816624..40819498,2	K562	blood:
10	chr21:40782804..40784995-chr21:40816330..40818172,2	K562	blood:
11	chr21:40553976..40556398-chr21:40816228..40819085,2	MCF-7	breast:
12	chr21:40758008..40760801-chr21:40816074..40819285,3	MCF-7	breast:
13	chr21:40757952..40760815-chr21:40812863..40817486,4	MCF-7	breast:
14	chr21:40719979..40722729-chr21:40816056..40819504,5	MCF-7	breast:
15	chr21:40759156..40760884-chr21:40816362..40818324,3	K562	blood:
16	chr21:40808687..40811589-chr21:40816980..40819320,3	K562	blood:
17	chr21:40720623..40723017-chr21:40815562..40818761,4	K562	blood:
18	chr21:40176263..40179138-chr21:40817088..40818717,2	K562	blood:
19	chr21:40683731..40685549-chr21:40816150..40817682,2	MCF-7	breast:
20	chr21:40555615..40557158-chr21:40816762..40818748,2	MCF-7	breast:
21	chr21:40719410..40723060-chr21:40814028..40819084,9	K562	blood:
22	chr21:40816254..40817919-chr21:40832845..40834906,2	MCF-7	breast:
23	chr21:40683837..40687545-chr21:40816624..40819639,6	K562	blood:

Variant related genes	Relation type
SH3BGR	TF binding region
LCA5L	TF binding region
ENSG00000185437	Chromatin interaction
ENSG00000157557	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11575944	0.95[ASN][1000 genomes]
rs12483547	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13051054	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13051142	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2049823	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837027	0.83[ASN][1000 genomes]
rs2837028	0.83[ASN][1000 genomes]
rs2837033	0.86[ASN][1000 genomes]
rs2837038	0.82[ASN][1000 genomes]
rs4816626	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4816628	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7276842	0.85[ASN][1000 genomes]
rs7277602	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7277633	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8130381	0.85[AMR][1000 genomes]
rs9979289	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9979353	0.82[ASN][1000 genomes]
rs9983100	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9983180	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9983404	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9983716	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs13050837	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs13050837	LCA5L	cis	Thyroid	GTEx
rs13050837	LCA5L	cis	Esophagus Muscularis	GTEx
rs13050837	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs13050837	WRB	cis	lung	GTEx
rs13050837	LCA5L	cis	Artery Aorta	GTEx
rs13050837	LCA5L	cis	Stomach	GTEx
rs13050837	LCA5L	cis	Muscle Skeletal	GTEx
rs13050837	WRB	cis	Artery Tibial	GTEx
rs13050837	WRB	cis	Thyroid	GTEx
rs13050837	LCA5L	cis	Artery Tibial	GTEx
rs13050837	LCA5L	cis	lung	GTEx
rs13050837	SH3BGR	cis	Thyroid	GTEx
rs13050837	LCA5L	cis	Nerve Tibial	GTEx
rs13050837	LCA5L	cis	Adipose Subcutaneous	GTEx
rs13050837	LCA5L	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40816400-40818200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr21:40816400-40818200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr21:40816600-40817400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr21:40816600-40817400	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr21:40816600-40817400	Flanking Active TSS	Brain Hippocampus Middle	brain
6	chr21:40816600-40817400	Flanking Active TSS	Fetal Muscle Trunk	muscle
7	chr21:40816600-40817400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr21:40816600-40817400	Flanking Active TSS	Dnd41	blood
9	chr21:40816600-40818200	Active TSS	H9 Cell Line	embryonic stem cell
10	chr21:40816600-40818200	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr21:40816600-40818400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr21:40816600-40818400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr21:40816600-40818400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr21:40816600-40818600	Active TSS	Brain Cingulate Gyrus	brain
15	chr21:40816800-40817400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr21:40816800-40817400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr21:40816800-40818000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr21:40816800-40818000	Active TSS	Fetal Heart	heart
19	chr21:40816800-40818000	Active TSS	HSMM	muscle
20	chr21:40816800-40818200	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr21:40816800-40818200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr21:40816800-40818200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr21:40816800-40818200	Active TSS	Colonic Mucosa	Colon
24	chr21:40816800-40818200	Active TSS	Lung	lung
25	chr21:40816800-40818200	Active TSS	NHDF-Ad	bronchial
26	chr21:40816800-40818400	Active TSS	Brain Germinal Matrix	brain
27	chr21:40816800-40818400	Active TSS	Right Atrium	heart
28	chr21:40816800-40818400	Active TSS	A549	lung
29	chr21:40816800-40818400	Active TSS	HSMMtube	muscle
30	chr21:40816800-40818600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr21:40817000-40817400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr21:40817000-40817400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr21:40817000-40817600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr21:40817000-40817800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr21:40817000-40817800	Active TSS	Thymus	Thymus
36	chr21:40817000-40817800	Active TSS	HMEC	breast
37	chr21:40817000-40818000	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr21:40817000-40818000	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr21:40817000-40818000	Active TSS	Muscle Satellite Cultured Cells	--
40	chr21:40817000-40818000	Active TSS	Fetal Lung	lung
41	chr21:40817000-40818000	Active TSS	Fetal Muscle Leg	muscle
42	chr21:40817000-40818000	Active TSS	Fetal Stomach	stomach
43	chr21:40817000-40818000	Active TSS	Osteobl	bone
44	chr21:40817000-40818200	Active TSS	H1 Cell Line	embryonic stem cell
45	chr21:40817000-40818200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr21:40817000-40818200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr21:40817000-40818200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr21:40817000-40818200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr21:40817000-40818200	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr21:40817000-40818200	Active TSS	iPS-15b Cell Line	embryonic stem cell

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