Variant report

Variant	rs2412823
Chromosome Location	chr15:44227270-44227271
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1053492	0.82[CEU][hapmap]
rs11070410	0.82[CEU][hapmap]
rs11070414	0.86[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs11638972	0.82[CEU][hapmap]
rs1545182	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2016840	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2306674	0.81[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2918945	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs3087657	0.84[ASW][hapmap];0.82[CEU][hapmap];0.89[LWK][hapmap]
rs524908	0.81[CEU][hapmap]
rs533143	0.82[CEU][hapmap]
rs575082	0.82[CEU][hapmap]
rs597705	0.81[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs638224	0.90[JPT][hapmap]
rs663214	0.84[ASW][hapmap];0.82[CEU][hapmap];0.89[LWK][hapmap]
rs693919	0.82[CEU][hapmap]
rs694461	0.82[CEU][hapmap]
rs7175129	0.82[CEU][hapmap]
rs920339	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
5	nsv1044435	chr15:44176103-44507403	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2412823	TGM5	cis	Lymphoblastoid	GTEx
rs2412823	ZNF690	cis	multi-tissue	Pritchard
rs2412823	ADAL	cis	parietal	SCAN
rs2412823	DUOX2	cis	parietal	SCAN
rs2412823	TGM5	cis	lymphoblastoid	seeQTL
rs2412823	SQRDL	cis	parietal	SCAN
rs2412823	STRC	cis	multi-tissue	Pritchard
rs2412823	CATSPER2	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44218600-44228400	Enhancers	Brain Substantia Nigra	brain
2	chr15:44220400-44227400	Enhancers	Brain Cingulate Gyrus	brain
3	chr15:44220400-44227600	Enhancers	Brain Hippocampus Middle	brain
4	chr15:44220800-44227400	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr15:44221200-44227400	Enhancers	Brain Anterior Caudate	brain
6	chr15:44224600-44227600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr15:44224800-44227400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr15:44225000-44227400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:44225000-44227400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr15:44225000-44228000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:44225000-44228200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:44225200-44232000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:44225400-44227400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:44225400-44246200	Weak transcription	Right Atrium	heart
15	chr15:44225600-44227400	Enhancers	NHDF-Ad	bronchial
16	chr15:44225600-44246200	Weak transcription	NH-A	brain
17	chr15:44226400-44227400	Enhancers	HSMMtube	muscle
18	chr15:44226400-44228000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:44227000-44227400	Enhancers	Fetal Heart	heart
20	chr15:44227200-44227400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:44227200-44233400	Weak transcription	Brain Angular Gyrus	brain
22	chr15:44227200-44251000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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