Variant report

Variant	rs56866897
Chromosome Location	chr21:40814605-40814606
allele	C/T
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40791594..40793834-chr21:40813541..40816112,2	K562	blood:
2	chr21:40552682..40557091-chr21:40814575..40819975,14	K562	blood:
3	chr21:40719238..40723494-chr21:40813785..40819496,7	MCF-7	breast:
4	chr21:40553201..40555417-chr21:40813842..40815672,2	MCF-7	breast:
5	chr21:40683646..40687466-chr21:40813293..40816602,5	MCF-7	breast:
6	chr21:40554820..40556384-chr21:40814358..40816122,2	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	chr21:40685795..40687913-chr21:40812651..40815254,2	K562	blood:
14	chr21:40719410..40723060-chr21:40814028..40819084,9	K562	blood:
15	chr21:40759083..40761929-chr21:40813666..40815597,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000255568	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000238141	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000157578	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs11575939	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16997618	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2065313	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205200	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205201	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223028	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246078	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2410128	0.93[AFR][1000 genomes];1.00[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	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837019	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837020	0.93[ASN][1000 genomes]
rs2837021	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837022	1.00[ASN][1000 genomes]
rs2837023	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837024	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837025	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837026	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837029	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837030	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837031	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837032	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837034	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837036	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837037	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837039	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837040	0.80[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	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56812456	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58900137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596289	0.80[ASN][1000 genomes]
rs61342945	0.95[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	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7277627	0.98[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	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73367928	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367958	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367962	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367976	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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs56866897	LCA5L	cis	Nerve Tibial	GTEx
rs56866897	LCA5L	cis	Esophagus Muscularis	GTEx
rs56866897	SH3BGR	cis	Artery Tibial	GTEx
rs56866897	LCA5L	cis	Artery Tibial	GTEx
rs56866897	LCA5L	cis	lung	GTEx
rs56866897	WRB	cis	Adipose Subcutaneous	GTEx
rs56866897	LCA5L	cis	Thyroid	GTEx
rs56866897	WRB	cis	Artery Tibial	GTEx
rs56866897	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs56866897	WRB	cis	lung	GTEx
rs56866897	WRB	cis	Nerve Tibial	GTEx
rs56866897	LCA5L	cis	Artery Aorta	GTEx
rs56866897	LCA5L	cis	Skin Sun Exposed Lower leg	GTEx
rs56866897	WRB	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:32 , 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	chr21:40813000-40814800	Enhancers	HSMM	muscle
10	chr21:40813000-40815400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr21:40813400-40816400	Weak transcription	Hela-S3	cervix
12	chr21:40813800-40814800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr21:40813800-40816600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr21:40813800-40816600	Enhancers	Fetal Heart	heart
15	chr21:40814000-40815000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr21:40814000-40815000	Enhancers	Fetal Muscle Leg	muscle
17	chr21:40814000-40816600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr21:40814000-40816600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr21:40814000-40816600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr21:40814000-40816600	Weak transcription	Right Ventricle	heart
21	chr21:40814200-40814800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr21:40814400-40814800	Flanking Active TSS	HSMMtube	muscle
23	chr21:40814400-40815000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr21:40814400-40816000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr21:40814400-40816600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr21:40814400-40816600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr21:40814600-40814800	Enhancers	Fetal Kidney	kidney
28	chr21:40814600-40815000	Weak transcription	K562	blood
29	chr21:40814600-40816400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr21:40814600-40816600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr21:40814600-40816600	Weak transcription	HMEC	breast
32	chr21:40814600-40816800	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links