Variant report

Variant	rs7139605
Chromosome Location	chr13:96811028-96811029
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs11616724	0.93[ASN][1000 genomes]
rs11618108	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11619636	0.82[ASN][1000 genomes]
rs12428062	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1327640	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16951448	0.82[ASN][1000 genomes]
rs1788062	1.00[JPT][hapmap]
rs1854174	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2257397	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2257398	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2262077	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2849439	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4547219	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4773932	0.82[ASN][1000 genomes]
rs490753	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs492247	0.85[AMR][1000 genomes]
rs492744	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493423	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs495214	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs502311	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs504340	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs526381	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs526702	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs531549	0.82[ASN][1000 genomes]
rs534010	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs534429	0.89[CEU][hapmap];0.91[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes]
rs537463	0.82[ASN][1000 genomes]
rs539293	0.87[AMR][1000 genomes]
rs540213	0.81[ASW][hapmap];0.89[CEU][hapmap];0.91[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs543775	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs544815	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs547858	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56077337	0.82[ASN][1000 genomes]
rs562879	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs564075	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs565297	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs565851	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs565898	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs568170	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs568945	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs571059	0.83[AMR][1000 genomes]
rs573909	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581462	0.85[AMR][1000 genomes]
rs593806	0.90[YRI][hapmap];0.81[AMR][1000 genomes]
rs602540	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626317	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs627074	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs639527	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs643302	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs645595	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs647811	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6492832	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6492833	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6492834	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649322	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs658705	0.81[AMR][1000 genomes]
rs661544	0.82[ASN][1000 genomes]
rs662884	0.89[CEU][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs672988	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs674565	0.89[CEU][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes]
rs675144	0.86[ASW][hapmap];0.89[CEU][hapmap];0.95[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs680576	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs680676	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs684902	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs686672	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72637840	0.93[ASN][1000 genomes]
rs72638023	0.93[ASN][1000 genomes]
rs72638024	0.93[ASN][1000 genomes]
rs72638031	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7318247	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7318449	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7330650	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7338171	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7338504	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7985150	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs816107	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs816109	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816142	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs9525134	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9525136	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1041165	chr13:96522021-96966520	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv869471	chr13:96622327-97223956	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv530390	chr13:96681439-97193029	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
6	nsv900936	chr13:96697209-97032483	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7139605	UGCGL2	cis	multi-tissue	Pritchard
rs7139605	UGGT2	cis	cerebellum	SCAN
rs7139605	DZIP1	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96800000-96816400	Weak transcription	Pancreas	Pancrea
2	chr13:96809400-96819200	Weak transcription	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links