Variant report

Variant	rs1564406
Chromosome Location	chr3:138133412-138133413
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1002766	0.82[YRI][hapmap]
rs12631438	0.83[CHD][hapmap]
rs1679153	0.83[CHD][hapmap]
rs1679177	0.83[CHD][hapmap]
rs1679181	0.83[CHD][hapmap]
rs1871398	0.88[ASN][1000 genomes]
rs1871516	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4550782	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626349	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs774013	0.91[ASN][1000 genomes]
rs9874855	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv1848610	chr3:138051423-138133412	Bivalent Enhancer Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1845560	chr3:138087467-138133412	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv460864	chr3:138100539-138194435	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv591853	chr3:138100539-138194435	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1564406	A4GNT	cis	parietal	SCAN
rs1564406	FAIM	cis	cerebellum	SCAN
rs1564406	ESYT3	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138124600-138136000	Weak transcription	Adipose Nuclei	Adipose
2	chr3:138125600-138136000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:138128000-138136600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:138128800-138136000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:138129200-138136000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:138130600-138133600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr3:138132000-138135400	Weak transcription	Osteobl	bone
8	chr3:138132200-138136000	Weak transcription	Right Atrium	heart
9	chr3:138132200-138136400	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:138132200-138136600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:138132400-138134400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:138132400-138136600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:138132400-138136600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:138132400-138136600	Weak transcription	HSMM	muscle
15	chr3:138132600-138136200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:138132800-138136200	Weak transcription	Fetal Heart	heart
17	chr3:138133200-138135600	Weak transcription	HSMMtube	muscle
18	chr3:138133200-138136600	Weak transcription	Left Ventricle	heart

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Input of quick search could be:

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

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