Variant report

Variant	rs9983716
Chromosome Location	chr21:40816940-40816941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:40816598-40818147	IMR90	lung:	n/a	n/a
2	POLR2A	chr21:40816939-40817109	ProgFib	skin:	n/a	n/a
3	MYC	chr21:40816901-40818552	K562	blood:	n/a	chr21:40817927-40817936
4	GATA2	chr21:40816678-40817858	SH-SY5Y	brain:	n/a	chr21:40817179-40817187
5	MAZ	chr21:40816767-40818164	IMR90	lung:	n/a	chr21:40817927-40817936
6	SMARCC1	chr21:40816551-40818214	Hela-S3	cervix:	n/a	n/a
7	MXI1	chr21:40816468-40818248	IMR90	lung:	n/a	n/a
8	REST	chr21:40816476-40818393	H1-neurons	neurons:	n/a	n/a
9	MXI1	chr21:40816307-40818898	SK-N-SH	brain:	n/a	n/a
10	HCFC1	chr21:40816914-40818182	K562	blood:	n/a	n/a
11	TEAD4	chr21:40816477-40818634	K562	blood:	n/a	n/a
12	BRCA1	chr21:40816496-40817143	Hela-S3	cervix:	n/a	n/a
13	SIN3AK20	chr21:40816478-40818410	MCF-7	breast:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

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

No data

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

Extended variants
information (count: 25 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11575944	0.95[ASN][1000 genomes]
rs12483547	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13050837	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13051054	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13051142	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2049823	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837014	0.81[AMR][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	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4816628	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7276842	0.85[ASN][1000 genomes]
rs7277602	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7277633	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8130381	0.87[AMR][1000 genomes]
rs9979289	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9979353	0.82[ASN][1000 genomes]
rs9983100	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9983180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9983404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv20340	chr21:40814284-40816976	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs9983716	LCA5L	cis	Muscle Skeletal	GTEx
rs9983716	LCA5L	cis	Adipose Subcutaneous	GTEx
rs9983716	LCA5L	cis	Artery Aorta	GTEx
rs9983716	LCA5L	cis	Thyroid	GTEx
rs9983716	LCA5L	cis	Artery Tibial	GTEx
rs9983716	WRB	cis	lung	GTEx
rs9983716	WRB	cis	Artery Tibial	GTEx
rs9983716	WRB	cis	Thyroid	GTEx
rs9983716	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs9983716	LCA5L	cis	lung	GTEx
rs9983716	LCA5L	cis	Esophagus Mucosa	GTEx
rs9983716	SH3BGR	cis	Thyroid	GTEx
rs9983716	LCA5L	cis	Esophagus Muscularis	GTEx
rs9983716	LCA5L	cis	Stomach	GTEx
rs9983716	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs9983716	LCA5L	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40816400-40817000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr21:40816400-40817000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr21:40816400-40817000	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr21:40816400-40817000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr21:40816400-40817000	Flanking Active TSS	Fetal Brain Female	brain
6	chr21:40816400-40817000	Enhancers	Placenta	Placenta
7	chr21:40816400-40817000	Flanking Active TSS	Osteobl	bone
8	chr21:40816400-40817200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr21:40816400-40817200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr21:40816400-40817200	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr21:40816400-40817200	Enhancers	Spleen	Spleen
12	chr21:40816400-40818200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr21:40816400-40818200	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr21:40816600-40817000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
15	chr21:40816600-40817000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr21:40816600-40817000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr21:40816600-40817000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr21:40816600-40817000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr21:40816600-40817000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr21:40816600-40817000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr21:40816600-40817000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr21:40816600-40817000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr21:40816600-40817000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
24	chr21:40816600-40817000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr21:40816600-40817000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr21:40816600-40817000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr21:40816600-40817000	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr21:40816600-40817000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr21:40816600-40817000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr21:40816600-40817000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr21:40816600-40817000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr21:40816600-40817000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr21:40816600-40817000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr21:40816600-40817000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr21:40816600-40817000	Enhancers	Esophagus	oesophagus
36	chr21:40816600-40817000	Flanking Active TSS	Fetal Intestine Large	intestine
37	chr21:40816600-40817000	Flanking Active TSS	Fetal Intestine Small	intestine
38	chr21:40816600-40817000	Flanking Active TSS	Fetal Kidney	kidney
39	chr21:40816600-40817000	Flanking Active TSS	Fetal Lung	lung
40	chr21:40816600-40817000	Flanking Active TSS	Fetal Muscle Leg	muscle
41	chr21:40816600-40817000	Flanking Active TSS	Fetal Stomach	stomach
42	chr21:40816600-40817000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr21:40816600-40817000	Flanking Active TSS	Right Ventricle	heart
44	chr21:40816600-40817000	Flanking Active TSS	HepG2	liver
45	chr21:40816600-40817000	Flanking Active TSS	HMEC	breast
46	chr21:40816600-40817000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
47	chr21:40816600-40817000	Flanking Active TSS	NHLF	lung
48	chr21:40816600-40817200	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr21:40816600-40817200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr21:40816600-40817200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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