Variant report

Variant	rs16950254
Chromosome Location	chr16:74950196-74950197
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	POLR2A	chr16:74950069-74950269	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
WDR59	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12447968	1.00[ASW][hapmap]
rs13335129	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16950325	1.00[CEU][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28691253	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7342703	0.86[CHB][hapmap]
rs8053634	0.89[EUR][1000 genomes]
rs9934255	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
3	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
4	nsv1058900	chr16:74753819-75005050	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv542958	chr16:74753819-75005050	Weak transcription Bivalent Enhancer Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	esv3345041	chr16:74756263-75066969	Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
7	nsv431516	chr16:74840166-75099566	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
9	nsv833280	chr16:74855811-75077227	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv1059764	chr16:74868327-74989488	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1064546	chr16:74868795-74989488	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv572977	chr16:74873513-74954897	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv526213	chr16:74873513-74990061	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv572978	chr16:74873574-74990004	Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv1063842	chr16:74896749-74990601	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv542959	chr16:74896749-74990601	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16950254	WWC3	trans	lymphoblastoid	RTeQTL
rs16950254	GSTO1	trans	lymphoblastoid	RTeQTL
rs16950254	CDC27	trans	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74905400-74950800	Strong transcription	Liver	Liver
2	chr16:74906200-74993200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:74937000-74956000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr16:74939600-74953000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr16:74939800-74951400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr16:74939800-74952800	Strong transcription	HepG2	liver
7	chr16:74939800-74958600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr16:74940000-74958600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr16:74940200-74950200	Strong transcription	HSMM	muscle
10	chr16:74940200-74950400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr16:74940200-74952800	Strong transcription	NH-A	brain
12	chr16:74940200-74955800	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr16:74940400-74950600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr16:74940400-74951400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr16:74940400-74952000	Strong transcription	Stomach Smooth Muscle	stomach
16	chr16:74940400-74953000	Strong transcription	Brain Cingulate Gyrus	brain
17	chr16:74940400-74955800	Strong transcription	Brain Anterior Caudate	brain
18	chr16:74940400-74956600	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr16:74940400-74957000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr16:74940600-74950800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
21	chr16:74940600-74951400	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr16:74940800-74956600	Strong transcription	Fetal Brain Female	brain
23	chr16:74941400-74950200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
24	chr16:74941800-74958600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr16:74942600-74951600	Strong transcription	Gastric	stomach
26	chr16:74944200-74950200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
27	chr16:74945000-74951400	Strong transcription	Brain Hippocampus Middle	brain
28	chr16:74945000-74955800	Strong transcription	Left Ventricle	heart
29	chr16:74945200-74950600	Strong transcription	HSMMtube	muscle
30	chr16:74945200-74951200	Strong transcription	Osteobl	bone
31	chr16:74945200-74951400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr16:74945200-74951400	Strong transcription	Brain Substantia Nigra	brain
33	chr16:74945200-74952000	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr16:74945200-74953000	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr16:74945200-74958600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr16:74945400-74950200	Strong transcription	Right Ventricle	heart
37	chr16:74945400-74952600	Strong transcription	NHDF-Ad	bronchial
38	chr16:74945800-74950200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
39	chr16:74945800-74950200	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr16:74945800-74951400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr16:74945800-74951400	Strong transcription	Colon Smooth Muscle	Colon
42	chr16:74945800-74953000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr16:74946000-74957200	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr16:74946200-74953200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr16:74946400-74955200	Weak transcription	NHLF	lung
46	chr16:74946400-74955400	Weak transcription	Fetal Heart	heart
47	chr16:74946600-74950800	Weak transcription	A549	lung
48	chr16:74947000-74950200	Strong transcription	Pancreas	Pancrea
49	chr16:74947000-74951000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr16:74947000-74951400	Strong transcription	Primary T killer memory cells from peripheral blood	blood

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