Variant report

Variant	rs498289
Chromosome Location	chr6:86116721-86116722
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57178197..57180890-chr6:86114463..86117112,2	MCF-7	breast:
2	chr6:86115836..86118735-chr6:86124270..86126196,2	K562	blood:

Extended variants
information (count: 145 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs1000632	0.90[ASN][1000 genomes]
rs1000633	0.90[ASN][1000 genomes]
rs1000634	0.90[ASN][1000 genomes]
rs11508041	0.85[ASN][1000 genomes]
rs11963844	0.85[ASN][1000 genomes]
rs11968230	0.85[ASN][1000 genomes]
rs11968238	0.85[ASN][1000 genomes]
rs12055597	0.90[ASN][1000 genomes]
rs12662033	0.85[ASN][1000 genomes]
rs12664908	0.82[ASN][1000 genomes]
rs1322401	0.90[ASN][1000 genomes]
rs1322403	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322404	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1570310	0.90[ASN][1000 genomes]
rs1570311	0.85[ASN][1000 genomes]
rs1590279	0.88[ASN][1000 genomes]
rs1590280	0.88[ASN][1000 genomes]
rs1665786	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1744121	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1744122	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2208722	0.90[ASN][1000 genomes]
rs2295890	0.85[ASN][1000 genomes]
rs313204	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs313206	0.94[ASN][1000 genomes]
rs4144166	0.84[ASN][1000 genomes]
rs4144167	0.82[ASN][1000 genomes]
rs4373339	0.84[ASN][1000 genomes]
rs4400191	0.84[ASN][1000 genomes]
rs4458647	0.85[ASN][1000 genomes]
rs4463232	0.85[ASN][1000 genomes]
rs4487548	0.85[ASN][1000 genomes]
rs4565270	0.84[ASN][1000 genomes]
rs4571538	0.85[ASN][1000 genomes]
rs4624841	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs490079	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494562	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494688	0.91[ASN][1000 genomes]
rs495469	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs495472	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515980	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520090	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521005	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs522129	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs522915	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527670	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs543359	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544403	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544408	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs547052	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs547963	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550499	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554113	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567686	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573737	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573892	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575477	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588823	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs589255	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59797285	0.85[ASN][1000 genomes]
rs617483	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618448	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs619299	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs619753	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630212	0.91[ASN][1000 genomes]
rs632163	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs637346	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638745	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640093	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643591	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs683218	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6919207	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs693077	0.94[ASN][1000 genomes]
rs6942065	0.84[ASN][1000 genomes]
rs727870	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7746186	0.84[ASN][1000 genomes]
rs7749745	0.90[ASN][1000 genomes]
rs7750970	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753022	0.82[ASN][1000 genomes]
rs7753711	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753936	0.90[ASN][1000 genomes]
rs7753950	0.90[ASN][1000 genomes]
rs7754559	0.90[ASN][1000 genomes]
rs7763191	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767626	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767800	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771860	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7772233	0.85[ASN][1000 genomes]
rs9294335	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9294336	0.85[ASN][1000 genomes]
rs9342039	0.85[ASN][1000 genomes]
rs9344518	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9344519	0.90[ASN][1000 genomes]
rs9344520	0.90[ASN][1000 genomes]
rs9344521	0.90[ASN][1000 genomes]
rs9344522	0.90[ASN][1000 genomes]
rs9344523	0.85[ASN][1000 genomes]
rs9344524	0.85[ASN][1000 genomes]
rs9344525	0.85[ASN][1000 genomes]
rs9344526	0.85[ASN][1000 genomes]
rs9344527	0.84[ASN][1000 genomes]
rs9344528	0.84[ASN][1000 genomes]
rs9344529	0.84[ASN][1000 genomes]
rs9353309	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9353310	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9353312	0.85[ASN][1000 genomes]
rs9353313	0.85[ASN][1000 genomes]
rs9353314	0.85[ASN][1000 genomes]
rs9353315	0.85[ASN][1000 genomes]
rs9353316	0.85[ASN][1000 genomes]
rs9353317	0.85[ASN][1000 genomes]
rs9359654	0.85[ASN][1000 genomes]
rs9359655	0.84[ASN][1000 genomes]
rs9362209	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9362211	0.90[ASN][1000 genomes]
rs9362212	0.88[ASN][1000 genomes]
rs9362213	0.90[ASN][1000 genomes]
rs9362214	0.88[ASN][1000 genomes]
rs9362215	0.90[ASN][1000 genomes]
rs9362216	0.85[ASN][1000 genomes]
rs9362217	0.85[ASN][1000 genomes]
rs9362218	0.85[ASN][1000 genomes]
rs9362219	0.85[ASN][1000 genomes]
rs9362220	0.85[ASN][1000 genomes]
rs9362221	0.85[ASN][1000 genomes]
rs9444342	0.82[ASN][1000 genomes]
rs9444343	0.82[ASN][1000 genomes]
rs9450260	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9450263	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9450269	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9450270	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9450271	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9450274	0.85[ASN][1000 genomes]
rs9450278	0.85[ASN][1000 genomes]
rs9450279	0.85[ASN][1000 genomes]
rs9450280	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
9	nsv463937	chr6:86114766-86264374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv604092	chr6:86114766-86264374	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs498289	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs498289	NT5E	cis	Whole Blood	GTEx
rs498289	NT5E	cis	Thyroid	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86113400-86131600	Weak transcription	Right Atrium	heart
2	chr6:86113800-86117800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:86113800-86118000	Enhancers	NHLF	lung
4	chr6:86114400-86118200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:86114600-86117600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:86114600-86118000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:86114600-86118200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:86115000-86117200	Enhancers	NHDF-Ad	bronchial
9	chr6:86115200-86117400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:86115200-86117600	Enhancers	HMEC	breast
11	chr6:86115400-86117000	Enhancers	Osteobl	bone
12	chr6:86115600-86116800	Enhancers	Hela-S3	cervix
13	chr6:86115600-86117000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:86115600-86117000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:86115600-86117200	Enhancers	Muscle Satellite Cultured Cells	--
16	chr6:86115600-86118000	Enhancers	NHEK	skin
17	chr6:86115600-86123200	Weak transcription	Ovary	ovary
18	chr6:86115800-86118200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:86115800-86118200	Enhancers	A549	lung
20	chr6:86116600-86116800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:86116600-86117400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:86116600-86117600	Weak transcription	Pancreas	Pancrea
23	chr6:86116600-86117600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:86116600-86118800	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links