Variant report

Variant	rs73367976
Chromosome Location	chr21:40813851-40813852
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	CTCF	chr21:40813800-40813950	SK-N-SH_RA	brain:	n/a	n/a
2	RAD21	chr21:40813286-40813884	MCF-7	breast:	n/a	chr21:40813613-40813632
3	RAD21	chr21:40813414-40813878	A549	lung:	n/a	chr21:40813613-40813632
4	EP300	chr21:40813456-40814109	K562	blood:	n/a	n/a
5	SMC3	chr21:40812876-40813953	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr21:40813319-40813930	K562	blood:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
7	RAD21	chr21:40813223-40814061	SK-N-SH	brain:	n/a	chr21:40813613-40813632
8	CTCF	chr21:40813358-40813917	K562	blood:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
9	CTCF	chr21:40813400-40813917	MCF-7	breast:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
10	ZC3H11A	chr21:40813485-40814088	K562	blood:	n/a	n/a
11	CTCF	chr21:40813760-40813910	HUVEC	blood vessel:	n/a	n/a
12	TBL1XR1	chr21:40813476-40814059	K562	blood:	n/a	n/a
13	TEAD4	chr21:40813369-40813852	K562	blood:	n/a	n/a
14	CTCF	chr21:40813408-40813885	GM12878	blood:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
15	RAD21	chr21:40813400-40813901	MCF-7	breast:	n/a	chr21:40813613-40813632
16	CTCF	chr21:40813220-40813993	SK-N-SH	brain:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
17	RAD21	chr21:40813418-40813879	HCT-116	colon:	n/a	chr21:40813613-40813632
18	CTCF	chr21:40813278-40813959	A549	lung:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
19	RAD21	chr21:40813384-40813859	HepG2	liver:	n/a	chr21:40813613-40813632

No.	Distal block	Cell Line	Cell type
1	chr21:40791594..40793834-chr21:40813541..40816112,2	K562	blood:
2	chr21:40719238..40723494-chr21:40813785..40819496,7	MCF-7	breast:
3	chr21:40177677..40179381-chr21:40812548..40814050,2	K562	blood:
4	chr21:40553201..40555417-chr21:40813842..40815672,2	MCF-7	breast:
5	chr21:40683646..40687466-chr21:40813293..40816602,5	MCF-7	breast:
6	chr21:40745299..40746167-chr21:40813543..40814094,2	MCF-7	breast:
7	chr21:40808402..40815127-chr21:40815513..40821149,12	K562	blood:
8	chr21:40757952..40760815-chr21:40812863..40817486,4	MCF-7	breast:
9	21:40748850-40752541..21:40812812-40815481	K562	blood:
10	chr21:40812406..40815051-chr21:40815498..40817690,4	K562	blood:
11	chr21:40808329..40812009-chr21:40812185..40815067,5	K562	blood:
12	chr21:40719600..40723122-chr21:40811701..40815528,3	K562	blood:
13	chr21:40768684..40769218-chr21:40813214..40814049,2	MCF-7	breast:
14	chr21:40685795..40687913-chr21:40812651..40815254,2	K562	blood:
15	chr21:40760487..40761081-chr21:40813246..40814131,2	MCF-7	breast:
16	chr21:40760349..40761906-chr21:40811512..40813865,2	K562	blood:
17	chr21:40759083..40761929-chr21:40813666..40815597,2	K562	blood:

Variant related genes	Relation type
LCA5L	TF binding region
SH3BGR	TF binding region
ENSG00000227406	Chromatin interaction
ENSG00000238141	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000157557	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000183527	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11575939	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16997618	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2065313	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205200	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205201	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223028	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246078	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2410128	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837009	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837015	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837017	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837018	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837019	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837020	0.97[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2837021	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837022	1.00[ASN][1000 genomes]
rs2837023	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837024	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837025	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837026	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837029	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837030	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837031	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837032	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837034	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837036	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837037	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837039	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837040	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2840267	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4281987	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56812456	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56866897	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58900137	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596289	0.80[ASN][1000 genomes]
rs61342945	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7275686	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7276575	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7276981	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7277627	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7279753	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73365952	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73367928	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367958	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367962	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367974	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73906032	0.81[ASN][1000 genomes]
rs73906033	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73906034	0.81[ASN][1000 genomes]
rs940625	0.80[ASN][1000 genomes]
rs9680443	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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs73367976	LCA5L	cis	Skin Sun Exposed Lower leg	GTEx
rs73367976	WRB	cis	Artery Tibial	GTEx
rs73367976	LCA5L	cis	Esophagus Muscularis	GTEx
rs73367976	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs73367976	LCA5L	cis	Artery Tibial	GTEx
rs73367976	LCA5L	cis	Artery Aorta	GTEx
rs73367976	LCA5L	cis	Thyroid	GTEx
rs73367976	WRB	cis	Nerve Tibial	GTEx
rs73367976	LCA5L	cis	Nerve Tibial	GTEx
rs73367976	LCA5L	cis	lung	GTEx
rs73367976	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs73367976	WRB	cis	Adipose Subcutaneous	GTEx
rs73367976	SH3BGR	cis	Artery Tibial	GTEx
rs73367976	WRB	cis	lung	GTEx

Chromatin state (count:25 , 50 per page) page: 1

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	chr21:40802600-40816200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr21:40802600-40816600	Weak transcription	Right Atrium	heart
5	chr21:40802800-40814000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr21:40809400-40816400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr21:40809800-40816600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr21:40811600-40816600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr21:40812600-40816600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr21:40813000-40814800	Enhancers	HSMM	muscle
11	chr21:40813000-40815400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr21:40813400-40814000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr21:40813400-40814000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr21:40813400-40816400	Weak transcription	Hela-S3	cervix
15	chr21:40813600-40814400	Enhancers	Fetal Kidney	kidney
16	chr21:40813600-40814600	Enhancers	Muscle Satellite Cultured Cells	--
17	chr21:40813800-40814000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr21:40813800-40814000	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr21:40813800-40814000	Flanking Active TSS	HSMMtube	muscle
20	chr21:40813800-40814400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr21:40813800-40814600	Enhancers	HMEC	breast
22	chr21:40813800-40814600	Enhancers	K562	blood
23	chr21:40813800-40814800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr21:40813800-40816600	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr21:40813800-40816600	Enhancers	Fetal Heart	heart

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