Variant report

Variant	rs4951684
Chromosome Location	chr1:211081891-211081892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10494930	1.00[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12082952	0.86[CHB][hapmap];0.84[GIH][hapmap];0.82[ASN][1000 genomes]
rs17017087	0.80[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs17017120	0.86[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap]
rs2062674	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4951489	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4951685	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4951690	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4951691	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4951692	0.80[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4951696	0.86[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4951705	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs6671566	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[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	nsv832503	chr1:210948760-211103163	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv873154	chr1:211057697-211117197	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv549124	chr1:211069694-211088474	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4951684	RD3	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211077000-211083000	Enhancers	Brain Hippocampus Middle	brain
2	chr1:211078400-211083000	Enhancers	Brain Substantia Nigra	brain
3	chr1:211078800-211082800	Enhancers	Brain Anterior Caudate	brain
4	chr1:211078800-211083800	Enhancers	HSMMtube	muscle
5	chr1:211079600-211082000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:211079800-211083000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:211079800-211083000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:211080400-211083000	Enhancers	Brain Angular Gyrus	brain
9	chr1:211080400-211085600	Enhancers	Liver	Liver
10	chr1:211080600-211082800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:211080800-211083000	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr1:211080800-211083800	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr1:211081000-211083000	Enhancers	Brain Cingulate Gyrus	brain
14	chr1:211081200-211083800	Weak transcription	HSMM	muscle

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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