Variant report

Variant	rs904809
Chromosome Location	chr16:69951291-69951292
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	TCF12	chr16:69951270-69952258	A549	lung:	n/a	n/a
2	MXI1	chr16:69951092-69952790	IMR90	lung:	n/a	chr16:69951845-69951854

Variant related genes	Relation type
WWP2	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 8 )

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	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11647767	0.95[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];0.85[TSI][hapmap];0.86[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]
rs4985376	0.88[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];0.95[TSI][hapmap];0.87[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];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985379	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985381	0.90[ASN][1000 genomes]
rs4985451	0.84[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];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985453	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985454	0.87[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];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985456	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]
rs4985459	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985461	0.85[ASN][1000 genomes]
rs61611907	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6499272	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499273	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7184994	0.85[ASN][1000 genomes]
rs7192245	0.88[EUR][1000 genomes]
rs7192483	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7193518	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7196525	0.86[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]
rs904810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302605	0.85[ASN][1000 genomes]
rs9746247	0.81[AMR][1000 genomes]
rs9922964	0.87[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs904809	CES8	cis	parietal	SCAN
rs904809	CLEC18A	cis	Thyroid	GTEx
rs904809	PDXDC2P	cis	Artery Tibial	GTEx
rs904809	CLEC18A	cis	Whole Blood	GTEx
rs904809	CLEC18A	cis	Adipose Subcutaneous	GTEx
rs904809	PDXDC2P	cis	parietal	SCAN
rs904809	CBFB	cis	parietal	SCAN
rs904809	COG4	cis	parietal	SCAN

Chromatin state (count:121 , 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	chr16:69923800-69951800	Weak transcription	GM12878-XiMat	blood
3	chr16:69924400-69965000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr16:69935200-69955000	Weak transcription	Colon Smooth Muscle	Colon
5	chr16:69938800-69951400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr16:69939000-69974000	Weak transcription	Fetal Brain Male	brain
7	chr16:69939600-69967600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr16:69940400-69958800	Weak transcription	Right Atrium	heart
9	chr16:69940800-69955000	Weak transcription	Psoas Muscle	Psoas
10	chr16:69943200-69965600	Weak transcription	Brain Germinal Matrix	brain
11	chr16:69943400-69958600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr16:69943400-69959400	Weak transcription	Pancreas	Pancrea
13	chr16:69943600-69951600	Weak transcription	Fetal Brain Female	brain
14	chr16:69943600-69951600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr16:69943600-69954800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr16:69943600-69954800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr16:69943600-69955000	Weak transcription	Brain Angular Gyrus	brain
18	chr16:69943600-69958800	Weak transcription	Right Ventricle	heart
19	chr16:69943600-69965000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr16:69943600-69967000	Weak transcription	Small Intestine	intestine
21	chr16:69944000-69957400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr16:69944000-69959200	Weak transcription	Stomach Mucosa	stomach
23	chr16:69944000-69959600	Weak transcription	Fetal Thymus	thymus
24	chr16:69945000-69951400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr16:69945200-69951600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr16:69945200-69954000	Weak transcription	Liver	Liver
27	chr16:69945200-69964600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr16:69945400-69951400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr16:69945400-69951400	Weak transcription	Fetal Intestine Large	intestine
30	chr16:69945400-69951600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr16:69945400-69953400	Weak transcription	Gastric	stomach
32	chr16:69945400-69954800	Weak transcription	Brain Substantia Nigra	brain
33	chr16:69945400-69955000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr16:69945400-69955200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr16:69945400-69964000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr16:69945600-69951400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr16:69945600-69951400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr16:69945600-69951800	Weak transcription	Brain Anterior Caudate	brain
39	chr16:69945600-69958800	Weak transcription	Colonic Mucosa	Colon
40	chr16:69945600-69959000	Weak transcription	Esophagus	oesophagus
41	chr16:69945600-69959000	Weak transcription	Thymus	Thymus
42	chr16:69945600-69969400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr16:69945800-69951400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr16:69945800-69954800	Weak transcription	Brain Hippocampus Middle	brain
45	chr16:69946000-69951600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr16:69946000-69953800	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr16:69946000-69959000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr16:69946400-69951800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr16:69947600-69977200	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr16:69948200-69955600	Strong transcription	Primary monocytes fromperipheralblood	blood

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