Variant report

Variant	rs2837039
Chromosome Location	chr21:40825555-40825556
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40825413..40827744-chr21:40969940..40971698,2	MCF-7	breast:
2	chr21:40720444..40722867-chr21:40823306..40826080,2	MCF-7	breast:
3	chr21:40823323..40825964-chr21:40833634..40835639,2	K562	blood:
4	chr21:40554460..40556456-chr21:40823248..40825971,3	K562	blood:
5	chr21:40759594..40762847-chr21:40823318..40826677,3	K562	blood:
6	chr21:40825465..40827848-chr21:40854649..40856447,2	K562	blood:
7	chr21:40554955..40557163-chr21:40823681..40826162,2	K562	blood:

Variant related genes	Relation type
ENSG00000185437	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000184809	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000272991	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10483056	1.00[CHD][hapmap]
rs11575939	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522	1.00[CHD][hapmap]
rs16997618	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16997765	1.00[CHD][hapmap]
rs16997780	1.00[CHD][hapmap]
rs2065313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223028	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246078	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2410128	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837009	0.92[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837015	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837017	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837020	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2837021	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837022	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2837023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837029	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837030	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837031	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837034	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837036	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837037	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837061	1.00[CHD][hapmap]
rs2837066	1.00[CHD][hapmap]
rs2840267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4281987	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56812456	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56866897	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58900137	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596289	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs61342945	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7275686	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7276418	1.00[CHD][hapmap]
rs7276575	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7276981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7277627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7279753	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73365952	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73367928	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367958	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367962	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367974	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367976	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73906032	0.81[ASN][1000 genomes]
rs73906033	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73906034	0.81[ASN][1000 genomes]
rs940625	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9680443	0.80[AMR][1000 genomes];0.91[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:22)

SNP	Gene	Cis/trans	Tissue	Source
rs2837039	SH3BGR	cis	Artery Tibial	GTEx
rs2837039	WRB	cis	Artery Tibial	GTEx
rs2837039	SH3BGR	cis	Adipose Subcutaneous	GTEx
rs2837039	WRB	cis	lung	GTEx
rs2837039	LCA5L	cis	Nerve Tibial	GTEx
rs2837039	LCA5L	cis	Thyroid	GTEx
rs2837039	LCA5L	cis	Artery Tibial	GTEx
rs2837039	BRWD1	cis	parietal	SCAN
rs2837039	SIM2	cis	parietal	SCAN
rs2837039	WRB	cis	cerebellum	SCAN
rs2837039	LCA5L	cis	Esophagus Muscularis	GTEx
rs2837039	NCRNA00114	cis	parietal	SCAN
rs2837039	WRB	cis	Nerve Tibial	GTEx
rs2837039	BRWD1	cis	cerebellum	SCAN
rs2837039	LCA5L	cis	lung	GTEx
rs2837039	IGSF5	cis	parietal	SCAN
rs2837039	WRB	cis	parietal	SCAN
rs2837039	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs2837039	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs2837039	LCA5L	cis	Skin Sun Exposed Lower leg	GTEx
rs2837039	WRB	cis	Adipose Subcutaneous	GTEx
rs2837039	SH3BGR	cis	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40822800-40828600	Active TSS	Right Ventricle	heart
2	chr21:40823000-40825800	Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr21:40823200-40825600	Active TSS	Right Atrium	heart
4	chr21:40823400-40825800	Active TSS	Brain Substantia Nigra	brain
5	chr21:40823600-40825800	Active TSS	Stomach Smooth Muscle	stomach
6	chr21:40823800-40825600	Active TSS	Fetal Heart	heart
7	chr21:40824000-40825600	Active TSS	Fetal Muscle Trunk	muscle
8	chr21:40824000-40852400	Weak transcription	Pancreas	Pancrea
9	chr21:40824600-40826800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr21:40824800-40826200	Weak transcription	Fetal Brain Male	brain
11	chr21:40824800-40828000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr21:40824800-40828400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr21:40825000-40826200	Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr21:40825000-40847800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr21:40825200-40825600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr21:40825200-40825600	Active TSS	Fetal Muscle Leg	muscle
17	chr21:40825200-40825600	Active TSS	HSMMtube	muscle
18	chr21:40825200-40826000	Enhancers	Brain Angular Gyrus	brain
19	chr21:40825200-40826400	Weak transcription	Left Ventricle	heart
20	chr21:40825200-40828400	Enhancers	Brain Cingulate Gyrus	brain
21	chr21:40825400-40825600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr21:40825400-40825600	Enhancers	Colon Smooth Muscle	Colon
23	chr21:40825400-40825800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr21:40825400-40826400	Weak transcription	Psoas Muscle	Psoas
25	chr21:40825400-40827800	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr21:40825400-40828000	Enhancers	K562	blood
27	chr21:40825400-40828600	Enhancers	Brain Hippocampus Middle	brain
28	chr21:40825400-40828800	Enhancers	Brain Anterior Caudate	brain
29	chr21:40825400-40829600	Weak transcription	Aorta	Aorta

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