Variant report

Variant	rs6499259
Chromosome Location	chr16:69863680-69863681
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10400956	0.96[ASN][1000 genomes]
rs10517	0.84[TSI][hapmap]
rs11075736	0.88[ASN][1000 genomes]
rs1139177	0.84[ASN][1000 genomes]
rs11862697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12019048	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12149920	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12921131	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1318651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16959059	1.00[CEU][hapmap];0.84[TSI][hapmap]
rs16959266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16959271	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16959272	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2088747	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291960	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2917667	1.00[CEU][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap]
rs2917669	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs2917681	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2917682	0.88[CEU][hapmap];0.85[GIH][hapmap]
rs2917683	0.88[CEU][hapmap]
rs2937120	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2937123	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2937126	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2937127	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2965753	1.00[CEU][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap]
rs2965756	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2965759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2965760	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2965761	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2965762	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965763	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965764	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790084	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3790085	0.81[YRI][hapmap]
rs3790087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3790088	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3826154	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs4247109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.89[ASN][1000 genomes]
rs4442796	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4608327	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[ASN][1000 genomes]
rs4619391	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.88[ASN][1000 genomes]
rs4985528	0.83[ASN][1000 genomes]
rs4985529	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985531	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61090597	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6499248	0.83[ASN][1000 genomes]
rs6499249	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6499250	0.84[ASN][1000 genomes]
rs689452	1.00[CEU][hapmap]
rs7188187	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204615	0.89[ASN][1000 genomes]
rs7359387	0.88[CEU][hapmap];0.82[MEX][hapmap]
rs8050369	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8057938	1.00[CEU][hapmap];0.88[ASN][1000 genomes]
rs8058594	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8062076	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9888980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9888981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9922223	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9927105	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9932486	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9940008	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1062171	chr16:69854267-70188585	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv542941	chr16:69854267-70188585	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1059249	chr16:69854467-70188446	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv542942	chr16:69854467-70188446	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2758428	chr16:69855122-70313222	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2758652	chr16:69855122-70313222	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6499259	NQO1	cis	multi-tissue	Pritchard
rs6499259	DDX28	cis	parietal	SCAN
rs6499259	GFOD2	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69823800-69874800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr16:69830600-69864200	Weak transcription	Colon Smooth Muscle	Colon
3	chr16:69830600-69867000	Weak transcription	Right Ventricle	heart
4	chr16:69833800-69864400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr16:69833800-69874600	Weak transcription	Dnd41	blood
6	chr16:69833800-69875600	Weak transcription	NHEK	skin
7	chr16:69834000-69910600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr16:69834200-69892200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr16:69836400-69867400	Weak transcription	Colonic Mucosa	Colon
10	chr16:69836800-69864200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr16:69836800-69864400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr16:69837000-69905600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr16:69837800-69864600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr16:69838600-69873000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr16:69838800-69864400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr16:69838800-69874400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr16:69846600-69874400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr16:69846600-69875200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr16:69852000-69864200	Strong transcription	Fetal Intestine Small	intestine
20	chr16:69852000-69893200	Weak transcription	K562	blood
21	chr16:69853000-69867600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr16:69853200-69864600	Weak transcription	Spleen	Spleen
23	chr16:69853200-69864800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr16:69853200-69867200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr16:69853200-69875000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr16:69853200-69878400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr16:69853400-69867000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr16:69853400-69867200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr16:69853400-69867200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr16:69853400-69867400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr16:69853400-69880000	Weak transcription	Hela-S3	cervix
32	chr16:69853600-69867200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr16:69855200-69867200	Weak transcription	HSMMtube	muscle
34	chr16:69855200-69873800	Weak transcription	HMEC	breast
35	chr16:69855200-69875600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr16:69855400-69864400	Weak transcription	Aorta	Aorta
37	chr16:69855400-69867200	Weak transcription	Placenta	Placenta
38	chr16:69855400-69867600	Weak transcription	Gastric	stomach
39	chr16:69855400-69874800	Weak transcription	Brain Germinal Matrix	brain
40	chr16:69855600-69864400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr16:69855600-69864400	Weak transcription	NHLF	lung
42	chr16:69855600-69864800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr16:69855600-69865200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr16:69855600-69867000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr16:69855600-69867000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr16:69855600-69867200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr16:69855600-69867200	Weak transcription	HSMM	muscle
48	chr16:69855600-69868800	Weak transcription	Fetal Brain Male	brain
49	chr16:69855600-69877000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr16:69856200-69875200	Weak transcription	Fetal Brain Female	brain

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