Variant report

Variant	rs6749506
Chromosome Location	chr2:145825390-145825391
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1006923	0.90[ASN][1000 genomes]
rs10206585	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10928241	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1125128	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12474485	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476764	0.86[EUR][1000 genomes]
rs12476923	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12477111	0.90[ASN][1000 genomes]
rs12691704	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12992411	0.90[ASN][1000 genomes]
rs12995180	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13015800	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384504	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13389190	0.90[ASN][1000 genomes]
rs13428423	0.90[ASN][1000 genomes]
rs1819055	0.88[EUR][1000 genomes]
rs1830318	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1830320	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1852686	0.86[EUR][1000 genomes]
rs1881409	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1881410	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252654	0.88[EUR][1000 genomes]
rs2663966	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34029033	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34372836	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35462154	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35805189	0.95[ASN][1000 genomes]
rs6430076	0.90[ASN][1000 genomes]
rs6430078	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6721988	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747171	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747275	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7423637	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562803	1.00[ASN][1000 genomes]
rs7604735	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7607110	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs787427	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs957292	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957293	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1002563	chr2:145182201-145863253	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv535957	chr2:145182201-145863253	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv932113	chr2:145515124-145844491	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv834398	chr2:145659419-145830156	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv431768	chr2:145741527-145981491	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6749506	PTPDC1	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:145819200-145826600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:145821400-145825400	Enhancers	Fetal Lung	lung
3	chr2:145821400-145827000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:145822000-145825800	Enhancers	NHDF-Ad	bronchial
5	chr2:145823000-145826200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:145824200-145830600	Weak transcription	Aorta	Aorta
7	chr2:145824600-145825400	Enhancers	Brain Hippocampus Middle	brain
8	chr2:145824600-145826200	Enhancers	Adipose Nuclei	Adipose
9	chr2:145824800-145825400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:145824800-145825400	Enhancers	Brain Angular Gyrus	brain
11	chr2:145825000-145825400	Enhancers	Brain Cingulate Gyrus	brain
12	chr2:145825200-145826200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:145825200-145827400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links