Variant report

Variant	rs4146604
Chromosome Location	chr2:48400165-48400166
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1112259	0.89[JPT][hapmap]
rs12469811	0.89[JPT][hapmap]
rs12713006	0.89[JPT][hapmap]
rs13010470	0.85[CEU][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap]
rs1396826	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs1546472	0.85[EUR][1000 genomes]
rs1567397	0.89[JPT][hapmap]
rs2086719	0.82[EUR][1000 genomes]
rs2175138	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs4953550	0.82[EUR][1000 genomes]
rs4953567	0.89[JPT][hapmap]
rs6545024	0.89[JPT][hapmap]
rs67114103	0.83[EUR][1000 genomes]
rs6751603	0.89[JPT][hapmap]
rs6755968	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs876871	0.89[JPT][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	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS 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 target site	36 gene(s)	inside rSNPs	diseases
3	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv581773	chr2:48277490-48443109	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4146604	PREPL	cis	parietal	SCAN
rs4146604	C2orf61	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48397000-48401800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr2:48397000-48401800	Weak transcription	Adipose Nuclei	Adipose
3	chr2:48397200-48401800	Weak transcription	Liver	Liver
4	chr2:48398000-48400800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr2:48398000-48401800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:48398400-48400200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:48399000-48400200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:48399000-48401800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:48399800-48401200	Enhancers	NHEK	skin
10	chr2:48399800-48402800	Enhancers	HMEC	breast
11	chr2:48400000-48400200	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr2:48400000-48401200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:48400000-48401200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:48400000-48403000	Enhancers	Primary monocytes fromperipheralblood	blood

Quick Search:

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

what's new

Quick links