Variant report

Variant	rs1077421
Chromosome Location	chr15:44236115-44236116
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1008183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11070413	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11070414	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs11070415	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11070416	1.00[ASN][1000 genomes]
rs11630936	0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs11631901	1.00[CHB][hapmap];0.87[JPT][hapmap];0.96[ASN][1000 genomes]
rs12439442	1.00[ASN][1000 genomes]
rs12440402	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12442168	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs1545182	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs16950215	0.92[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs2016837	1.00[CEU][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs2412822	1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs28542819	0.90[ASN][1000 genomes]
rs28548859	0.98[EUR][1000 genomes]
rs28685813	0.81[ASN][1000 genomes]
rs2918945	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2918946	0.97[EUR][1000 genomes]
rs3850777	0.92[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs4544217	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs472797	0.97[EUR][1000 genomes]
rs530074	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs563940	1.00[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs589649	0.97[EUR][1000 genomes]
rs597705	1.00[CEU][hapmap];0.96[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs638224	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs678513	1.00[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs7178452	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs747714	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8042714	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs920339	1.00[CEU][hapmap];0.97[EUR][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1077421	ADAL	cis	Esophagus Muscularis	GTEx
rs1077421	ADAL	cis	Adipose Subcutaneous	GTEx
rs1077421	ADAL	cis	Thyroid	GTEx
rs1077421	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs1077421	CKMT1A	cis	Esophagus Mucosa	GTEx
rs1077421	TGM5	cis	lymphoblastoid	seeQTL
rs1077421	ADAL	cis	Artery Tibial	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44225400-44246200	Weak transcription	Right Atrium	heart
2	chr15:44225600-44246200	Weak transcription	NH-A	brain
3	chr15:44227200-44251000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:44227400-44244200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:44229000-44245000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:44234200-44241000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr15:44234800-44237800	Weak transcription	GM12878-XiMat	blood
8	chr15:44234800-44238400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr15:44235000-44239000	Weak transcription	Brain Angular Gyrus	brain
10	chr15:44235000-44242400	Weak transcription	Brain Substantia Nigra	brain
11	chr15:44235200-44238800	Weak transcription	Brain Hippocampus Middle	brain
12	chr15:44235600-44236400	Enhancers	Osteobl	bone
13	chr15:44235600-44236600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr15:44235600-44236600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:44235600-44236600	Enhancers	NHDF-Ad	bronchial
16	chr15:44235600-44236800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:44235800-44236200	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr15:44235800-44236400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:44235800-44236400	Enhancers	HSMMtube	muscle
20	chr15:44235800-44236400	Enhancers	NHLF	lung
21	chr15:44235800-44236600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:44236000-44236200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:44236000-44236400	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links