Variant report

Variant	rs494688
Chromosome Location	chr6:86100089-86100090
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr6:86100089-86100406	HepG2	liver:	n/a	n/a
2	FOXA1	chr6:86099850-86100495	HepG2	liver:	n/a	n/a
3	HDAC2	chr6:86099836-86100167	HepG2	liver:	n/a	n/a
4	HNF4G	chr6:86099871-86100128	HepG2	liver:	n/a	n/a
5	HNF4A	chr6:86100033-86100462	HepG2	liver:	n/a	chr6:86100271-86100284 chr6:86100271-86100284
6	EP300	chr6:86099738-86100371	HepG2	liver:	n/a	n/a
7	SP1	chr6:86099823-86100459	HepG2	liver:	n/a	n/a
8	ARID3A	chr6:86099918-86100702	HepG2	liver:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNX14-1	chr6:86099731-86100095	NONHSAT113834

Variant related genes	Relation type
ENSG00000234155	TF binding region

Extended variants
information (count: 120 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1000632	0.82[ASN][1000 genomes]
rs1000633	0.82[ASN][1000 genomes]
rs1000634	0.82[ASN][1000 genomes]
rs12055597	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12528808	0.82[JPT][hapmap]
rs12662033	0.85[JPT][hapmap]
rs12664908	0.85[JPT][hapmap]
rs1322401	0.82[ASN][1000 genomes]
rs1322403	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1322404	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1570310	0.82[ASN][1000 genomes]
rs1570311	0.85[JPT][hapmap]
rs1590279	0.85[JPT][hapmap]
rs1665786	0.91[ASN][1000 genomes]
rs1744121	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1744122	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2208722	0.82[ASN][1000 genomes]
rs313204	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs313206	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3812137	0.85[JPT][hapmap]
rs3812139	0.85[JPT][hapmap]
rs4144167	0.85[JPT][hapmap]
rs4373339	0.85[JPT][hapmap]
rs4400191	0.85[JPT][hapmap]
rs4458647	0.85[JPT][hapmap]
rs4487548	0.85[JPT][hapmap]
rs4565270	0.85[JPT][hapmap]
rs4624841	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs490079	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs494562	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs495469	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs495472	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs498289	0.91[ASN][1000 genomes]
rs515980	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs520090	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs521005	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs522129	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs522915	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs527670	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs543359	0.91[ASN][1000 genomes]
rs544403	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs544408	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs547052	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs547963	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs550499	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs554113	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs567686	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs573737	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs573892	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs575477	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs588823	0.82[AMR][1000 genomes]
rs589255	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs617483	0.91[ASN][1000 genomes]
rs618448	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs619299	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs619753	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs630212	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs632163	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs637346	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs638745	0.91[ASN][1000 genomes]
rs640093	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs643591	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs683218	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6900270	0.85[JPT][hapmap]
rs6902904	0.85[JPT][hapmap]
rs6910543	0.85[JPT][hapmap]
rs6913634	0.85[JPT][hapmap]
rs6919207	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs693077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6942065	0.85[JPT][hapmap]
rs727870	0.85[ASN][1000 genomes]
rs7744309	0.85[JPT][hapmap]
rs7745560	0.85[JPT][hapmap]
rs7749745	0.82[ASN][1000 genomes]
rs7750970	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7753022	0.85[JPT][hapmap]
rs7753711	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7753936	0.82[ASN][1000 genomes]
rs7753950	0.82[ASN][1000 genomes]
rs7754559	0.82[ASN][1000 genomes]
rs7763191	0.91[ASN][1000 genomes]
rs7767626	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7767800	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7771187	0.82[JPT][hapmap]
rs7771366	0.85[JPT][hapmap]
rs7771860	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9294335	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9344518	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9344519	0.82[ASN][1000 genomes]
rs9344520	0.82[ASN][1000 genomes]
rs9344521	0.82[ASN][1000 genomes]
rs9344522	0.82[ASN][1000 genomes]
rs9344530	0.85[JPT][hapmap]
rs9353309	0.91[ASN][1000 genomes]
rs9353310	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9353319	0.85[JPT][hapmap]
rs9359655	0.85[JPT][hapmap]
rs9359656	0.85[JPT][hapmap]
rs9362209	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9362211	0.82[ASN][1000 genomes]
rs9362213	0.82[ASN][1000 genomes]
rs9362215	0.82[ASN][1000 genomes]
rs9362223	0.85[JPT][hapmap]
rs9450260	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450263	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450269	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450270	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450271	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450278	0.85[JPT][hapmap]
rs9450280	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9450286	0.85[JPT][hapmap]
rs9450294	0.85[JPT][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs494688	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs494688	NT5E	cis	Thyroid	GTEx
rs494688	NT5E	cis	Whole Blood	GTEx
rs494688	NT5E	cis	lymphoblastoid	seeQTL
rs494688	SYNCRIP	cis	parietal	SCAN

Chromatin state (count:28 , 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	chr6:86097000-86100600	Active TSS	Duodenum Mucosa	Duodenum
3	chr6:86097400-86102600	Enhancers	Fetal Intestine Large	intestine
4	chr6:86098400-86101600	Enhancers	HepG2	liver
5	chr6:86099000-86100800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:86099000-86100800	Enhancers	Pancreas	Pancrea
7	chr6:86099200-86101200	Enhancers	A549	lung
8	chr6:86099200-86104600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:86099400-86100200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:86099400-86101200	Enhancers	Stomach Mucosa	stomach
11	chr6:86099600-86100800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:86099600-86100800	Enhancers	HMEC	breast
13	chr6:86099600-86101000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:86099600-86101000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:86099600-86101000	Enhancers	NHDF-Ad	bronchial
16	chr6:86099600-86101000	Enhancers	NHEK	skin
17	chr6:86099800-86100800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:86099800-86100800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:86099800-86100800	Enhancers	Osteobl	bone
20	chr6:86099800-86101000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:86099800-86101000	Enhancers	Muscle Satellite Cultured Cells	--
22	chr6:86099800-86101000	Enhancers	HSMM	muscle
23	chr6:86099800-86103200	Enhancers	Fetal Intestine Small	intestine
24	chr6:86100000-86100400	Enhancers	Liver	Liver
25	chr6:86100000-86100600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr6:86100000-86101000	Enhancers	NHLF	lung
27	chr6:86100000-86101200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr6:86100000-86103800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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