Variant report

Variant	rs4493083
Chromosome Location	chr16:75294589-75294590
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	chr16:75294293-75294593	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:75259384..75262203-chr16:75293212..75295661,2	K562	blood:

Variant related genes	Relation type
BCAR1	TF binding region
ENSG00000240338	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11149810	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11538269	0.92[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap];0.81[EUR][1000 genomes]
rs11640470	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1862737	0.92[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5842	0.89[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7197999	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8062565	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1056082	chr16:75004990-75295847	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv833282	chr16:75154171-75330634	Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv516504	chr16:75223491-75306402	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv523405	chr16:75227969-75342846	Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	esv1806781	chr16:75235390-75307470	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv906909	chr16:75236154-75316074	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	esv1792587	chr16:75237936-75305783	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv906910	chr16:75251299-75316074	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv906911	chr16:75252526-75296247	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv906912	chr16:75252526-75320827	Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	esv1813349	chr16:75257361-75302684	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
15	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
16	nsv906913	chr16:75267743-75306402	Genic enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
17	nsv471095	chr16:75269533-75320827	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
18	esv1843498	chr16:75271642-75296844	Genic enhancers Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4493083	CFDP1	cis	cerebellum	SCAN
rs4493083	SF3B3	cis	parietal	SCAN
rs4493083	FUK	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75286000-75297400	Enhancers	Psoas Muscle	Psoas
2	chr16:75286000-75297600	Genic enhancers	Fetal Intestine Small	intestine
3	chr16:75286000-75298000	Genic enhancers	Fetal Stomach	stomach
4	chr16:75289000-75297400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr16:75289200-75298600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr16:75289400-75295000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr16:75290000-75297800	Weak transcription	Fetal Kidney	kidney
8	chr16:75290200-75295800	Weak transcription	Small Intestine	intestine
9	chr16:75290800-75294600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr16:75291000-75295000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr16:75291000-75295400	Weak transcription	Aorta	Aorta
12	chr16:75291000-75295400	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr16:75291200-75295400	Weak transcription	A549	lung
14	chr16:75291600-75295800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr16:75292000-75294600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr16:75292000-75295400	Weak transcription	Esophagus	oesophagus
17	chr16:75292200-75295200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr16:75292200-75295800	Weak transcription	Stomach Mucosa	stomach
19	chr16:75292200-75296000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr16:75292200-75298600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr16:75292400-75294600	Weak transcription	Osteobl	bone
22	chr16:75292400-75295000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr16:75292400-75295000	Weak transcription	Gastric	stomach
24	chr16:75292400-75295400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr16:75292600-75294800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr16:75292600-75295200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr16:75292600-75296000	Weak transcription	HSMM	muscle
28	chr16:75292600-75298200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr16:75292800-75294600	Weak transcription	NH-A	brain
30	chr16:75292800-75294800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr16:75292800-75295000	Weak transcription	Brain Germinal Matrix	brain
32	chr16:75292800-75295000	Weak transcription	Right Atrium	heart
33	chr16:75292800-75295800	Weak transcription	HSMMtube	muscle
34	chr16:75292800-75296000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr16:75293000-75294600	Weak transcription	Liver	Liver
36	chr16:75293000-75294800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr16:75293000-75294800	Weak transcription	Fetal Brain Female	brain
38	chr16:75293000-75294800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr16:75293000-75295000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr16:75293000-75295000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr16:75293000-75295000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr16:75293000-75295000	Weak transcription	Left Ventricle	heart
43	chr16:75293000-75295000	Weak transcription	Lung	lung
44	chr16:75293000-75295000	Weak transcription	Ovary	ovary
45	chr16:75293000-75295200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr16:75293000-75295200	Weak transcription	Brain Substantia Nigra	brain
47	chr16:75293000-75295200	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr16:75293200-75294600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr16:75293200-75294600	Weak transcription	Fetal Heart	heart
50	chr16:75293200-75294800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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