Variant report

Variant	rs984682
Chromosome Location	chr2:63345921-63345922
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10206947	0.82[ASW][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap];0.83[YRI][hapmap]
rs1025131	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs11899838	0.83[GIH][hapmap]
rs12615947	0.85[GIH][hapmap]
rs13389366	0.84[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes]
rs1829524	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2138798	0.85[GIH][hapmap]
rs2162014	0.89[CHB][hapmap];0.83[CHD][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs2421860	0.94[ASW][hapmap];0.84[GIH][hapmap];0.90[LWK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs4316930	0.82[ASW][hapmap]
rs4671457	0.90[CHB][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.84[ASN][1000 genomes]
rs6728488	0.84[CEU][hapmap];0.91[AFR][1000 genomes]
rs7603593	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv2756598	chr2:63085848-63491438	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	esv3340700	chr2:63127412-63534998	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1004678	chr2:63230722-63562484	Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs984682	BAG1	trans	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63342600-63349600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:63343600-63349600	Weak transcription	Primary T cells from cord blood	blood
3	chr2:63344200-63348000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr2:63344400-63346000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:63344400-63350600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:63344400-63360400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:63344800-63350200	Weak transcription	Fetal Stomach	stomach
8	chr2:63345400-63346400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
9	chr2:63345400-63346400	Strong transcription	Brain Hippocampus Middle	brain
10	chr2:63345600-63346400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:63345800-63346400	Strong transcription	Fetal Brain Female	brain
12	chr2:63345800-63346600	Strong transcription	Left Ventricle	heart
13	chr2:63345800-63348000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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