Variant report

Variant	rs9450263
Chromosome Location	chr6:86097702-86097703
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:86095318..86098285-chr6:86101304..86103572,2	K562	blood:
2	chr6:86097062..86098574-chr6:86102355..86104381,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNX14-1	chr6:86096939-86099275	XLOC_005777
2	lnc-SNX14-1	chr6:86096937-86099275	ENSG00000234155
3	lnc-SNX14-1	chr6:86096965-86099275	NONHSAT113834

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1000632	0.84[ASN][1000 genomes]
rs1000633	0.84[ASN][1000 genomes]
rs1000634	0.84[ASN][1000 genomes]
rs12055597	0.84[ASN][1000 genomes]
rs1322401	0.84[ASN][1000 genomes]
rs1322403	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1322404	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1570310	0.84[ASN][1000 genomes]
rs1590279	0.82[ASN][1000 genomes]
rs1590280	0.82[ASN][1000 genomes]
rs1665786	0.94[ASN][1000 genomes]
rs1744121	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1744122	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2208722	0.84[ASN][1000 genomes]
rs313204	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313206	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4624841	0.94[ASN][1000 genomes]
rs490079	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs494562	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs494688	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs495469	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs495472	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs498289	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs515980	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs520090	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs521005	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs522129	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs522915	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs527670	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs543359	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs544403	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs544408	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs547052	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs547963	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs550499	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs554113	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs567686	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs573737	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs573892	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs575477	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs588823	0.85[AMR][1000 genomes]
rs589255	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs617483	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs618448	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs619299	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs619753	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs630212	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs632163	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs637346	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs638745	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs640093	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs643591	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683218	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6919207	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs693077	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727870	0.88[ASN][1000 genomes]
rs7749745	0.84[ASN][1000 genomes]
rs7750970	0.94[ASN][1000 genomes]
rs7753711	0.94[ASN][1000 genomes]
rs7753936	0.84[ASN][1000 genomes]
rs7753950	0.84[ASN][1000 genomes]
rs7754559	0.84[ASN][1000 genomes]
rs7763191	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7767626	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7767800	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7771860	0.94[ASN][1000 genomes]
rs9294335	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9344518	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9344519	0.84[ASN][1000 genomes]
rs9344520	0.84[ASN][1000 genomes]
rs9344521	0.84[ASN][1000 genomes]
rs9344522	0.84[ASN][1000 genomes]
rs9353309	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9353310	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9362209	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9362211	0.84[ASN][1000 genomes]
rs9362212	0.82[ASN][1000 genomes]
rs9362213	0.84[ASN][1000 genomes]
rs9362214	0.82[ASN][1000 genomes]
rs9362215	0.84[ASN][1000 genomes]
rs9450260	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450269	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450270	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450271	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017418	chr6:85344786-86259540	Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv538347	chr6:85344786-86259540	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv830721	chr6:85987644-86147414	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3326486	chr6:86020165-86292456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1019960	chr6:86023236-86136666	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3435075	chr6:86052235-86271910	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9450263	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs9450263	NT5E	cis	Whole Blood	GTEx
rs9450263	NT5E	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86087600-86111200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:86093200-86097800	Weak transcription	Fetal Intestine Small	intestine
3	chr6:86093400-86098400	Weak transcription	HepG2	liver
4	chr6:86093400-86099000	Weak transcription	Small Intestine	intestine
5	chr6:86095800-86099400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:86095800-86099600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:86096000-86099000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:86096400-86099800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:86097000-86098200	Enhancers	Liver	Liver
10	chr6:86097000-86099600	Weak transcription	NHEK	skin
11	chr6:86097000-86100600	Active TSS	Duodenum Mucosa	Duodenum
12	chr6:86097200-86100000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr6:86097400-86102600	Enhancers	Fetal Intestine Large	intestine
14	chr6:86097600-86098000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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