Variant report

Variant	rs904808
Chromosome Location	chr16:69958495-69958496
allele	A/G
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	chr16:69958404-69958566	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:69957939..69963004-chr16:69963560..69969238,6	K562	blood:
2	chr16:69956564..69958821-chr16:69961060..69963505,2	K562	blood:
3	chr16:69955657..69958548-chr16:69969251..69971948,2	K562	blood:

Variant related genes	Relation type
WWP2	TF binding region
ENSG00000208017	Chromatin interaction
ENSG00000198373	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10048088	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10048090	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1052429	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11864678	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12932078	0.87[EUR][1000 genomes]
rs12932286	0.85[EUR][1000 genomes]
rs1566452	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1833933	0.82[CHB][hapmap]
rs1862662	0.82[CHB][hapmap]
rs1983016	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs2102066	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2270840	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2270841	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2270842	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2291961	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2362643	1.00[JPT][hapmap]
rs2362658	1.00[JPT][hapmap]
rs3748388	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3762177	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs3762178	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4985377	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4985378	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4985381	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4985392	0.82[CHB][hapmap]
rs4985452	1.00[JPT][hapmap]
rs4985455	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4985456	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4985461	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7184994	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7203489	0.82[CHB][hapmap]
rs7206222	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8047818	0.95[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8048590	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8048678	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8049004	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8052727	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8052838	0.82[CHB][hapmap]
rs904803	1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs904804	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs904805	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs904806	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs904807	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs904809	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs904810	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9302605	0.80[ASN][1000 genomes]
rs933696	0.82[CHB][hapmap]

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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs904808	CLEC18A	cis	Whole Blood	GTEx
rs904808	CLEC18A	cis	Adipose Subcutaneous	GTEx
rs904808	CLEC18A	cis	Skin Sun Exposed Lower leg	GTEx
rs904808	RP11-419C5.2	cis	Nerve Tibial	GTEx
rs904808	PDXDC2P	cis	Esophagus Muscularis	GTEx
rs904808	CLEC18A	cis	Thyroid	GTEx
rs904808	PDXDC2P	cis	Heart Left Ventricle	GTEx
rs904808	PDXDC2P	cis	Artery Tibial	GTEx
rs904808	CLEC18A	cis	Esophagus Mucosa	GTEx
rs904808	PDXDC2P	cis	Nerve Tibial	GTEx
rs904808	CLEC18A	cis	Esophagus Muscularis	GTEx
rs904808	CLEC18A	cis	lung	GTEx
rs904808	RP11-419C5.2	cis	Artery Tibial	GTEx

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	chr16:69924400-69965000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr16:69939000-69974000	Weak transcription	Fetal Brain Male	brain
4	chr16:69939600-69967600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr16:69940400-69958800	Weak transcription	Right Atrium	heart
6	chr16:69943200-69965600	Weak transcription	Brain Germinal Matrix	brain
7	chr16:69943400-69958600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr16:69943400-69959400	Weak transcription	Pancreas	Pancrea
9	chr16:69943600-69958800	Weak transcription	Right Ventricle	heart
10	chr16:69943600-69965000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr16:69943600-69967000	Weak transcription	Small Intestine	intestine
12	chr16:69944000-69959200	Weak transcription	Stomach Mucosa	stomach
13	chr16:69944000-69959600	Weak transcription	Fetal Thymus	thymus
14	chr16:69945200-69964600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr16:69945400-69964000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr16:69945600-69958800	Weak transcription	Colonic Mucosa	Colon
17	chr16:69945600-69959000	Weak transcription	Esophagus	oesophagus
18	chr16:69945600-69959000	Weak transcription	Thymus	Thymus
19	chr16:69945600-69969400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr16:69946000-69959000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr16:69947600-69977200	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr16:69948200-69977400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr16:69948400-69977400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr16:69952200-69958600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr16:69952200-69958800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr16:69952200-69959800	Weak transcription	GM12878-XiMat	blood
27	chr16:69952200-69961000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr16:69952200-69965000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr16:69952400-69963800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr16:69952600-69958800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr16:69952600-69958800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr16:69952600-69958800	Weak transcription	HSMMtube	muscle
33	chr16:69952600-69958800	Weak transcription	HUVEC	blood vessel
34	chr16:69952600-69959000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr16:69952600-69959000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr16:69952600-69959400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr16:69952600-69959400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr16:69952600-69959400	Weak transcription	Spleen	Spleen
39	chr16:69952600-69963600	Weak transcription	NHEK	skin
40	chr16:69952600-69976000	Weak transcription	Hela-S3	cervix
41	chr16:69952800-69958800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr16:69952800-69958800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr16:69952800-69958800	Weak transcription	HMEC	breast
44	chr16:69952800-69959000	Weak transcription	Placenta	Placenta
45	chr16:69952800-69959200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr16:69952800-69963200	Weak transcription	Fetal Brain Female	brain
47	chr16:69952800-69965000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr16:69952800-69966800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr16:69953600-69974800	Weak transcription	A549	lung
50	chr16:69954000-69958600	Enhancers	NHDF-Ad	bronchial

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