Variant report

Variant	rs4985456
Chromosome Location	chr16:69952657-69952658
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10048088	0.90[ASN][1000 genomes]
rs10048090	0.90[ASN][1000 genomes]
rs1052429	0.82[CHB][hapmap];0.83[CHD][hapmap];0.85[ASN][1000 genomes]
rs11645233	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11647767	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11864678	0.90[ASN][1000 genomes]
rs12932078	0.85[ASN][1000 genomes]
rs1566452	0.82[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1983016	0.82[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs2102066	0.90[ASN][1000 genomes]
rs2270840	0.90[ASN][1000 genomes]
rs2270841	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2270842	0.82[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs2291961	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2362643	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2362658	1.00[JPT][hapmap]
rs3748388	0.82[CHB][hapmap];0.83[CHD][hapmap];0.85[ASN][1000 genomes]
rs3762177	0.82[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs3762178	0.90[ASN][1000 genomes]
rs41454046	0.80[YRI][hapmap]
rs4985376	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4985377	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985379	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985381	0.90[ASN][1000 genomes]
rs4985451	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985452	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985453	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985454	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985459	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985461	0.85[ASN][1000 genomes]
rs61611907	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6499272	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499273	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7184994	0.85[ASN][1000 genomes]
rs7192245	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7192483	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7193518	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7196525	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7206222	0.90[ASN][1000 genomes]
rs8047818	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8048590	0.82[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8048678	0.82[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8049004	0.90[ASN][1000 genomes]
rs8052727	0.90[ASN][1000 genomes]
rs904803	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs904804	0.90[ASN][1000 genomes]
rs904805	0.90[ASN][1000 genomes]
rs904806	0.90[ASN][1000 genomes]
rs904807	0.82[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs904808	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs904809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs904810	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302605	0.85[ASN][1000 genomes]
rs9922964	0.92[AMR][1000 genomes];0.82[EUR][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	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
8	esv1792580	chr16:69950347-70005207	Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	esv1801278	chr16:69951043-70050770	Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
10	esv1829103	chr16:69951043-70050770	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4985456	COG4	cis	parietal	SCAN
rs4985456	EXOSC6	cis	multi-tissue	Pritchard
rs4985456	PDXDC2P	cis	Artery Tibial	GTEx
rs4985456	CLEC18A	cis	Thyroid	GTEx
rs4985456	CBFB	cis	parietal	SCAN
rs4985456	CES8	cis	parietal	SCAN
rs4985456	COG4	cis	brain	seeQTL
rs4985456	LOC497190	cis	multi-tissue	Pritchard
rs4985456	VAC14	cis	lymphoblastoid	seeQTL
rs4985456	PDXDC2P	cis	parietal	SCAN
rs4985456	LOC440349	cis	multi-tissue	Pritchard
rs4985456	CLEC18A	cis	Adipose Subcutaneous	GTEx
rs4985456	MGC34761	cis	multi-tissue	Pritchard
rs4985456	CLEC18A	cis	Whole Blood	GTEx
rs4985456	CLEC18A	cis	lung	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69911400-69970200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr16:69924400-69965000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr16:69935200-69955000	Weak transcription	Colon Smooth Muscle	Colon
4	chr16:69939000-69974000	Weak transcription	Fetal Brain Male	brain
5	chr16:69939600-69967600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr16:69940400-69958800	Weak transcription	Right Atrium	heart
7	chr16:69940800-69955000	Weak transcription	Psoas Muscle	Psoas
8	chr16:69943200-69965600	Weak transcription	Brain Germinal Matrix	brain
9	chr16:69943400-69958600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr16:69943400-69959400	Weak transcription	Pancreas	Pancrea
11	chr16:69943600-69954800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr16:69943600-69954800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr16:69943600-69955000	Weak transcription	Brain Angular Gyrus	brain
14	chr16:69943600-69958800	Weak transcription	Right Ventricle	heart
15	chr16:69943600-69965000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr16:69943600-69967000	Weak transcription	Small Intestine	intestine
17	chr16:69944000-69957400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr16:69944000-69959200	Weak transcription	Stomach Mucosa	stomach
19	chr16:69944000-69959600	Weak transcription	Fetal Thymus	thymus
20	chr16:69945200-69954000	Weak transcription	Liver	Liver
21	chr16:69945200-69964600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr16:69945400-69953400	Weak transcription	Gastric	stomach
23	chr16:69945400-69954800	Weak transcription	Brain Substantia Nigra	brain
24	chr16:69945400-69955000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr16:69945400-69955200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr16:69945400-69964000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr16:69945600-69958800	Weak transcription	Colonic Mucosa	Colon
28	chr16:69945600-69959000	Weak transcription	Esophagus	oesophagus
29	chr16:69945600-69959000	Weak transcription	Thymus	Thymus
30	chr16:69945600-69969400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr16:69945800-69954800	Weak transcription	Brain Hippocampus Middle	brain
32	chr16:69946000-69953800	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr16:69946000-69959000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr16:69947600-69977200	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr16:69948200-69955600	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr16:69948200-69977400	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr16:69948400-69956800	Strong transcription	Primary T cells from cord blood	blood
38	chr16:69948400-69977400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr16:69949800-69952800	Enhancers	Placenta	Placenta
40	chr16:69951200-69954400	Strong transcription	Duodenum Mucosa	Duodenum
41	chr16:69951600-69952800	Strong transcription	Fetal Brain Female	brain
42	chr16:69951600-69955200	Weak transcription	Left Ventricle	heart
43	chr16:69951600-69957800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr16:69951800-69952800	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr16:69951800-69953200	Weak transcription	Fetal Stomach	stomach
46	chr16:69951800-69954000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr16:69951800-69957800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr16:69952000-69954600	Strong transcription	Fetal Intestine Large	intestine
49	chr16:69952000-69954800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr16:69952200-69952800	Enhancers	HUES64 Cell Line	embryonic stem cell

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