Variant report

Variant	rs2063998
Chromosome Location	chr21:40816185-40816186
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 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	chr21:40683646..40687466-chr21:40813293..40816602,5	MCF-7	breast:
7	chr21:40758008..40760801-chr21:40816074..40819285,3	MCF-7	breast:
8	chr21:40757952..40760815-chr21:40812863..40817486,4	MCF-7	breast:
9	chr21:40719979..40722729-chr21:40816056..40819504,5	MCF-7	breast:
10	chr21:40720623..40723017-chr21:40815562..40818761,4	K562	blood:
11	chr21:40683731..40685549-chr21:40816150..40817682,2	MCF-7	breast:
12	chr21:40719410..40723060-chr21:40814028..40819084,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000182093	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000183527	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs2065313	0.86[YRI][hapmap]
rs2246078	0.86[YRI][hapmap]
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]
rs2837018	0.86[YRI][hapmap]
rs2837019	0.84[YRI][hapmap]
rs2837020	0.86[YRI][hapmap]
rs2837023	0.84[YRI][hapmap]
rs2837024	0.84[YRI][hapmap]
rs2837026	0.84[YRI][hapmap]
rs2837030	0.86[YRI][hapmap]
rs2837032	0.84[YRI][hapmap]
rs2837034	0.86[YRI][hapmap]
rs2837035	0.88[CHB][hapmap];0.84[JPT][hapmap];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	0.88[CHB][hapmap];0.85[JPT][hapmap];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]
rs7277627	0.84[YRI][hapmap]
rs73367984	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367987	0.96[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
rs2063998	LCA5L	cis	Esophagus Mucosa	GTEx
rs2063998	LCA5L	cis	Artery Aorta	GTEx
rs2063998	LCA5L	cis	lung	GTEx
rs2063998	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs2063998	LCA5L	cis	Esophagus Muscularis	GTEx
rs2063998	SH3BGR	cis	Thyroid	GTEx
rs2063998	SH3BGR	cis	Artery Tibial	GTEx
rs2063998	LCA5L	cis	Artery Tibial	GTEx
rs2063998	LCA5L	cis	Nerve Tibial	GTEx
rs2063998	LCA5L	cis	Thyroid	GTEx

Chromatin state (count:37 , 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	chr21:40809400-40816400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr21:40809800-40816600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr21:40811600-40816600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr21:40812600-40816600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr21:40813400-40816400	Weak transcription	Hela-S3	cervix
10	chr21:40813800-40816600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr21:40813800-40816600	Enhancers	Fetal Heart	heart
12	chr21:40814000-40816600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr21:40814000-40816600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr21:40814000-40816600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr21:40814000-40816600	Weak transcription	Right Ventricle	heart
16	chr21:40814400-40816600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr21:40814400-40816600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr21:40814600-40816400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr21:40814600-40816600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr21:40814600-40816600	Weak transcription	HMEC	breast
21	chr21:40814600-40816800	Weak transcription	Ovary	ovary
22	chr21:40814800-40816400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr21:40814800-40816400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr21:40814800-40816600	Weak transcription	HSMM	muscle
25	chr21:40815000-40816400	Weak transcription	Fetal Muscle Leg	muscle
26	chr21:40815000-40816600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr21:40815000-40816600	Weak transcription	Fetal Kidney	kidney
28	chr21:40815200-40816200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr21:40815400-40816400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr21:40815400-40816400	Weak transcription	Spleen	Spleen
31	chr21:40815800-40816200	Weak transcription	HSMMtube	muscle
32	chr21:40815800-40816200	Weak transcription	K562	blood
33	chr21:40815800-40816800	Enhancers	Fetal Thymus	thymus
34	chr21:40816000-40816400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr21:40816000-40816600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr21:40816000-40816600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
37	chr21:40816000-40816600	Enhancers	Brain Anterior Caudate	brain

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