Variant report

Variant	rs1616107
Chromosome Location	chr5:127135609-127135610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1002214	0.81[AMR][1000 genomes]
rs10044507	0.98[ASN][1000 genomes]
rs10066288	0.81[AMR][1000 genomes]
rs10067219	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1067705	0.81[AMR][1000 genomes]
rs1092294	0.81[AMR][1000 genomes]
rs1213745	0.81[AMR][1000 genomes]
rs13155734	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1356121	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1432641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1432642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2673770	0.81[AMR][1000 genomes]
rs6867166	1.00[ASW][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.90[LWK][hapmap];0.97[MKK][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6878186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs711361	0.81[AMR][1000 genomes]
rs711363	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs711364	1.00[CEU][hapmap]
rs711369	0.81[AMR][1000 genomes]
rs7729013	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs790829	0.89[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes]
rs790834	0.81[AMR][1000 genomes]
rs790839	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs790840	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs790841	0.80[AFR][1000 genomes]
rs796919	0.81[AMR][1000 genomes]
rs806464	0.81[AMR][1000 genomes]
rs810996	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1616107	PRRC1	cis	cerebellum	SCAN
rs1616107	CTXN3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127128200-127137400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:127130000-127136600	Weak transcription	Gastric	stomach
3	chr5:127131800-127136600	Weak transcription	Stomach Mucosa	stomach
4	chr5:127134200-127136000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:127134600-127136000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:127134800-127135800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr5:127134800-127136000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:127135000-127137400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:127135200-127143800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:127135400-127135800	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr5:127135400-127138200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:127135600-127137400	Weak transcription	NHEK	skin
13	chr5:127135600-127137600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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