Variant report

Variant	rs2837040
Chromosome Location	chr21:40826615-40826616
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40816194..40819113-chr21:40826557..40830216,3	K562	blood:
2	chr21:40825413..40827744-chr21:40969940..40971698,2	MCF-7	breast:
3	chr21:40821968..40825719-chr21:40825995..40830907,7	K562	blood:
4	chr21:40759594..40762847-chr21:40823318..40826677,3	K562	blood:
5	chr21:40820536..40825890-chr21:40826084..40828688,4	K562	blood:
6	chr21:40825465..40827848-chr21:40854649..40856447,2	K562	blood:

Variant related genes	Relation type
ENSG00000184809	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000157578	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	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16997618	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2065313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[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];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223028	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2410128	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837009	0.93[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837015	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837017	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[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];0.92[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];0.92[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];0.92[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];0.92[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];0.92[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];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837029	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837031	0.81[AMR][1000 genomes];0.92[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];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837034	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837036	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837037	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837039	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]
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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4281987	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56812456	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56866897	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58900137	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596289	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs61342945	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7275686	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
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];0.92[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];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7279753	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73365952	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73367928	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367958	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367962	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367974	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367976	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73906032	0.81[ASN][1000 genomes]
rs73906033	0.81[AMR][1000 genomes];0.87[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];0.92[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
rs2837040	SH3BGR	cis	Artery Tibial	GTEx
rs2837040	LCA5L	cis	Nerve Tibial	GTEx
rs2837040	WRB	cis	Nerve Tibial	GTEx
rs2837040	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs2837040	WRB	cis	Artery Tibial	GTEx
rs2837040	LCA5L	cis	Thyroid	GTEx
rs2837040	WRB	cis	lung	GTEx
rs2837040	LCA5L	cis	Artery Tibial	GTEx
rs2837040	LCA5L	cis	Skin Sun Exposed Lower leg	GTEx
rs2837040	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs2837040	WRB	cis	Adipose Subcutaneous	GTEx
rs2837040	SH3BGR	cis	Adipose Subcutaneous	GTEx
rs2837040	LCA5L	cis	lung	GTEx
rs2837040	LCA5L	cis	Esophagus Muscularis	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40822800-40828600	Active TSS	Right Ventricle	heart
2	chr21:40824000-40852400	Weak transcription	Pancreas	Pancrea
3	chr21:40824600-40826800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr21:40824800-40828000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr21:40824800-40828400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr21:40825000-40847800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr21:40825200-40828400	Enhancers	Brain Cingulate Gyrus	brain
8	chr21:40825400-40827800	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr21:40825400-40828000	Enhancers	K562	blood
10	chr21:40825400-40828600	Enhancers	Brain Hippocampus Middle	brain
11	chr21:40825400-40828800	Enhancers	Brain Anterior Caudate	brain
12	chr21:40825400-40829600	Weak transcription	Aorta	Aorta
13	chr21:40825600-40828200	Enhancers	Fetal Muscle Leg	muscle
14	chr21:40825600-40836800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr21:40825800-40828600	Enhancers	Brain Substantia Nigra	brain
16	chr21:40825800-40828800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr21:40826000-40827400	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr21:40826000-40828000	Flanking Active TSS	Fetal Heart	heart
19	chr21:40826200-40827000	Enhancers	Fetal Brain Male	brain
20	chr21:40826200-40828800	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr21:40826400-40827600	Enhancers	Psoas Muscle	Psoas
22	chr21:40826400-40827600	Enhancers	Right Atrium	heart
23	chr21:40826400-40828600	Enhancers	Left Ventricle	heart
24	chr21:40826400-40828800	Enhancers	Brain Angular Gyrus	brain
25	chr21:40826600-40827000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr21:40826600-40827200	Enhancers	Stomach Smooth Muscle	stomach
27	chr21:40826600-40827400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr21:40826600-40849800	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links