Variant report

Variant	rs73367984
Chromosome Location	chr21:40816499-40816500
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr21:40816468-40816662	K562	blood:	n/a	n/a
2	POLR2A	chr21:40816294-40816549	K562	blood:	n/a	n/a
3	MXI1	chr21:40816468-40818248	IMR90	lung:	n/a	n/a
4	REST	chr21:40816476-40818393	H1-neurons	neurons:	n/a	n/a
5	MXI1	chr21:40816307-40818898	SK-N-SH	brain:	n/a	n/a
6	RCOR1	chr21:40816457-40816895	K562	blood:	n/a	n/a
7	TEAD4	chr21:40816477-40818634	K562	blood:	n/a	n/a
8	BRCA1	chr21:40816496-40817143	Hela-S3	cervix:	n/a	n/a
9	SIN3AK20	chr21:40816478-40818410	MCF-7	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr21:40816464-40816514	AG09309	skin:	n/a
2	chr21:40816464-40816514	HMEC	breast:	n/a
3	chr21:40816464-40816514	H1-hESC	embryonic stem cell:	embryo
4	chr21:40816464-40816514	Caco-2	colon:	n/a
5	chr21:40816464-40816514	NHDF-neo	bronchial:	n/a
6	chr21:40816464-40816514	HPAEpiC	pulmonary alveolar:	n/a
7	chr21:40816464-40816514	ProgFib	skin:	n/a
8	chr21:40816464-40816514	NH-A	brain:	n/a
9	chr21:40816464-40816514	HNPCEpiC	eye:	n/a
10	chr21:40816464-40816514	CMK	blood:	n/a
11	chr21:40816464-40816514	SK-N-SH	brain:	n/a
12	chr21:40816464-40816514	HCF	heart:	n/a
13	chr21:40816464-40816514	T-47D	breast:	n/a
14	chr21:40816464-40816514	BE2_C	brain:	n/a
15	chr21:40816464-40816514	HIPEpiC	eye:	n/a
16	chr21:40816464-40816514	ovcar-3	ovarian:	n/a
17	chr21:40816464-40816514	SK-N-MC	brain:	n/a
18	chr21:40816464-40816514	LNCaP	prostate:	n/a
19	chr21:40816464-40816514	MCF-7	breast:	n/a
20	chr21:40816464-40816514	GM19239	blood:	n/a
21	chr21:40816464-40816514	GM12878	blood:	n/a
22	chr21:40816464-40816514	HEEpiC	esophagus:	n/a
23	chr21:40816464-40816514	SK-N-SH_RA	brain:	n/a
24	chr21:40816464-40816514	HL-60	blood:	n/a
25	chr21:40816464-40816514	Hepatocyte	liver:	n/a
26	chr21:40816464-40816514	AG04449	skin:	fetal
27	chr21:40816464-40816514	AG04450	lung:	fetal
28	chr21:40816464-40816514	SAEC	small airway:	n/a
29	chr21:40816464-40816514	HRCEpiC	kidney:	n/a
30	chr21:40816464-40816514	Hela-S3	cervix:	n/a
31	chr21:40816464-40816514	HCM	heart:	n/a
32	chr21:40816464-40816514	HRE	kidney:	n/a
33	chr21:40816464-40816514	AG10803	skin:	n/a
34	chr21:40816464-40816514	PFSK-1	brain:	n/a
35	chr21:40816464-40816514	Jurkat	blood:	n/a
36	chr21:40816464-40816514	U87	brain:	n/a
37	chr21:40816464-40816514	NHBE	bronchial:	n/a
38	chr21:40816464-40816514	A549	lung:	n/a
39	chr21:40816464-40816514	GM12892	blood:	n/a
40	chr21:40816464-40816514	K562	blood:	n/a
41	chr21:40816464-40816514	GM12891	blood:	n/a
42	chr21:40816464-40816514	ECC-1	luminal epithelium:	n/a
43	chr21:40816464-40816514	IMR90	lung:	fetal
44	chr21:40816464-40816514	HepG2	liver:	n/a
45	chr21:40816464-40816514	BJ	skin:	n/a
46	chr21:40816464-40816514	RPTEC	kidney:	n/a
47	chr21:40816464-40816514	GM06990	blood:	n/a
48	chr21:40816464-40816514	HCT-116	colon:	n/a
49	chr21:40816464-40816514	HCPEpiC	choroid plexus:	n/a
50	chr21:40816464-40816514	NT2-D1	testis:	n/a

(count:17 , 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	chr21:40683646..40687466-chr21:40813293..40816602,5	MCF-7	breast:
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	chr21:40719410..40723060-chr21:40814028..40819084,9	K562	blood:
17	chr21:40816254..40817919-chr21:40832845..40834906,2	MCF-7	breast:

No data

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

Extended variants
information (count: 14 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2063998	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277787	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2410158	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2837035	0.82[ASN][1000 genomes]
rs35286554	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35360199	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3787926	0.81[ASN][1000 genomes]
rs60838770	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71316676	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71316677	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73367987	0.97[AFR][1000 genomes];0.99[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs73367984	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs73367984	LCA5L	cis	lung	GTEx
rs73367984	SH3BGR	cis	Artery Tibial	GTEx
rs73367984	LCA5L	cis	Nerve Tibial	GTEx
rs73367984	LCA5L	cis	Esophagus Muscularis	GTEx
rs73367984	LCA5L	cis	Thyroid	GTEx
rs73367984	LCA5L	cis	Artery Aorta	GTEx
rs73367984	LCA5L	cis	Artery Tibial	GTEx
rs73367984	LCA5L	cis	Esophagus Mucosa	GTEx
rs73367984	SH3BGR	cis	Thyroid	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40778200-40816600	Weak transcription	Pancreas	Pancrea
2	chr21:40778400-40816600	Weak transcription	Left Ventricle	heart
3	chr21:40802600-40816600	Weak transcription	Right Atrium	heart
4	chr21:40809800-40816600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr21:40811600-40816600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr21:40812600-40816600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr21:40813800-40816600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr21:40813800-40816600	Enhancers	Fetal Heart	heart
9	chr21:40814000-40816600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr21:40814000-40816600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr21:40814000-40816600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr21:40814000-40816600	Weak transcription	Right Ventricle	heart
13	chr21:40814400-40816600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr21:40814400-40816600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr21:40814600-40816600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr21:40814600-40816600	Weak transcription	HMEC	breast
17	chr21:40814600-40816800	Weak transcription	Ovary	ovary
18	chr21:40814800-40816600	Weak transcription	HSMM	muscle
19	chr21:40815000-40816600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr21:40815000-40816600	Weak transcription	Fetal Kidney	kidney
21	chr21:40815800-40816800	Enhancers	Fetal Thymus	thymus
22	chr21:40816000-40816600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr21:40816000-40816600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
24	chr21:40816000-40816600	Enhancers	Brain Anterior Caudate	brain
25	chr21:40816200-40816600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr21:40816200-40816600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr21:40816200-40816600	Enhancers	Dnd41	blood
28	chr21:40816200-40816600	Enhancers	K562	blood
29	chr21:40816200-40816800	Enhancers	Placenta Amnion	Placenta Amnion
30	chr21:40816400-40816600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr21:40816400-40816600	Enhancers	H9 Cell Line	embryonic stem cell
32	chr21:40816400-40816600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr21:40816400-40816600	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr21:40816400-40816600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
35	chr21:40816400-40816600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr21:40816400-40816600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr21:40816400-40816600	Enhancers	Primary hematopoietic stem cells	blood
38	chr21:40816400-40816600	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr21:40816400-40816600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr21:40816400-40816600	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr21:40816400-40816600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr21:40816400-40816600	Enhancers	Adipose Nuclei	Adipose
43	chr21:40816400-40816600	Enhancers	Brain Angular Gyrus	brain
44	chr21:40816400-40816600	Enhancers	Brain Germinal Matrix	brain
45	chr21:40816400-40816600	Enhancers	Brain Hippocampus Middle	brain
46	chr21:40816400-40816600	Enhancers	Colon Smooth Muscle	Colon
47	chr21:40816400-40816600	Enhancers	Duodenum Mucosa	Duodenum
48	chr21:40816400-40816600	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr21:40816400-40816600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr21:40816400-40816600	Enhancers	Fetal Brain Male	brain

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