Variant report

Variant	rs13337037
Chromosome Location	chr16:31478711-31478712
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	POLR2A	chr16:31478669-31478814	GM12878	blood:	n/a	n/a
2	RUNX3	chr16:31478401-31478857	GM12878	blood:	n/a	n/a
3	MAX	chr16:31478422-31479038	NB4	blood:	n/a	chr16:31478849-31478858 chr16:31478847-31478860 chr16:31478844-31478863 chr16:31478848-31478859 chr16:31478847-31478860
4	SP1	chr16:31478457-31478827	GM12878	blood:	n/a	n/a
5	EBF1	chr16:31478467-31478843	GM12878	blood:	n/a	chr16:31478648-31478659 chr16:31478649-31478659
6	POLR2A	chr16:31478657-31478736	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr16:31478710-31478788	K562	blood:	n/a	n/a
8	EBF1	chr16:31478408-31478843	GM12878	blood:	n/a	chr16:31478648-31478659 chr16:31478649-31478659
9	MYC	chr16:31478307-31478957	NB4	blood:	n/a	chr16:31478849-31478858 chr16:31478847-31478860 chr16:31478844-31478863 chr16:31478848-31478859 chr16:31478847-31478860
10	RUNX3	chr16:31478443-31478873	GM12878	blood:	n/a	n/a
11	POLR2A	chr16:31478212-31479236	GM12878	blood:	n/a	n/a
12	WRNIP1	chr16:31478543-31478772	GM12878	blood:	n/a	n/a
13	SP1	chr16:31478431-31478855	GM12878	blood:	n/a	n/a
14	POLR2A	chr16:31478412-31478854	HL-60	blood:	n/a	n/a
15	POLR2A	chr16:31478474-31478995	GM12892	blood:	n/a	n/a
16	EBF1	chr16:31478457-31478792	GM12878	blood:	n/a	chr16:31478648-31478659 chr16:31478649-31478659
17	POLR2A	chr16:31478445-31478819	GM12891	blood:	n/a	n/a
18	POLR2A	chr16:31478132-31479927	HepG2	liver:	n/a	n/a
19	POLR2A	chr16:31478413-31479003	HepG2	liver:	n/a	n/a
20	EP300	chr16:31478578-31478784	GM12878	blood:	n/a	n/a
21	POLR2A	chr16:31477993-31479137	GM12878	blood:	n/a	n/a
22	POLR2A	chr16:31478241-31478958	HepG2	liver:	n/a	n/a
23	BHLHE40	chr16:31478531-31478754	GM12878	blood:	n/a	n/a
24	POLR2A	chr16:31478432-31479001	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:31475154..31478732-chr16:31483245..31485698,3	MCF-7	breast:
2	chr16:31188773..31190894-chr16:31477404..31479097,2	K562	blood:

Variant related genes	Relation type
TGFB1I1	TF binding region
ENSG00000140682	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11150626	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11865835	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs13143	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28641848	0.83[AMR][1000 genomes]
rs34081766	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934739	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4519345	1.00[JPT][hapmap]
rs4889548	1.00[JPT][hapmap]
rs4889673	1.00[JPT][hapmap]
rs6565235	0.96[EUR][1000 genomes]
rs6565236	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6565242	1.00[JPT][hapmap]
rs7188278	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72789337	0.80[AMR][1000 genomes]
rs8057401	1.00[JPT][hapmap]
rs8062314	0.96[EUR][1000 genomes]
rs9926717	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9934336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9935222	1.00[JPT][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	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
2	nsv833194	chr16:31358179-31528545	Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases
4	nsv905748	chr16:31427678-31559220	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
5	nsv905749	chr16:31427678-31565597	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	96 gene(s)	inside rSNPs	diseases
6	nsv905750	chr16:31427678-31587662	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases
7	nsv905751	chr16:31431360-31489033	Bivalent Enhancer Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
8	nsv905752	chr16:31436932-31565597	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	95 gene(s)	inside rSNPs	diseases
9	nsv905753	chr16:31436932-31587662	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
10	nsv905754	chr16:31451699-31565597	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13337037	INO80E	cis	parietal	SCAN
rs13337037	TAOK2	cis	parietal	SCAN
rs13337037	AC026471.6	cis	lung	GTEx
rs13337037	PRR14	cis	cerebellum	SCAN
rs13337037	SLC5A2	cis	lung	GTEx
rs13337037	FBXL19	cis	cerebellum	SCAN
rs13337037	AHSP	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31471000-31482600	Weak transcription	Small Intestine	intestine
2	chr16:31471800-31483000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr16:31472000-31480400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr16:31472000-31481800	Weak transcription	NHDF-Ad	bronchial
5	chr16:31472000-31482000	Weak transcription	Fetal Heart	heart
6	chr16:31472000-31482400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr16:31472000-31482400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr16:31472000-31482600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr16:31472000-31482600	Weak transcription	Stomach Mucosa	stomach
10	chr16:31472600-31479000	Strong transcription	Adipose Nuclei	Adipose
11	chr16:31472600-31479000	Strong transcription	Fetal Intestine Small	intestine
12	chr16:31472600-31482600	Weak transcription	Fetal Brain Male	brain
13	chr16:31472600-31483000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr16:31472800-31478800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr16:31472800-31478800	Strong transcription	Esophagus	oesophagus
16	chr16:31472800-31482400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr16:31472800-31482400	Weak transcription	Hela-S3	cervix
18	chr16:31472800-31482400	Weak transcription	HMEC	breast
19	chr16:31472800-31482400	Weak transcription	HSMM	muscle
20	chr16:31473000-31479000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr16:31473000-31479000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr16:31473000-31479000	Strong transcription	Fetal Stomach	stomach
23	chr16:31473200-31478800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr16:31473200-31478800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr16:31473200-31478800	Strong transcription	Brain Hippocampus Middle	brain
26	chr16:31473200-31478800	Strong transcription	Gastric	stomach
27	chr16:31473200-31478800	Strong transcription	Ovary	ovary
28	chr16:31473200-31478800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr16:31473200-31479000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr16:31473200-31479000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr16:31473200-31479000	Strong transcription	Brain Anterior Caudate	brain
32	chr16:31473200-31479000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr16:31473200-31479000	Strong transcription	NHLF	lung
34	chr16:31473200-31479200	Strong transcription	Fetal Brain Female	brain
35	chr16:31473200-31479400	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr16:31473400-31478800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr16:31473400-31478800	Strong transcription	Brain Cingulate Gyrus	brain
38	chr16:31473400-31478800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr16:31473400-31478800	Strong transcription	Colonic Mucosa	Colon
40	chr16:31473400-31478800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr16:31473400-31478800	Strong transcription	Pancreas	Pancrea
42	chr16:31473400-31478800	Strong transcription	Rectal Smooth Muscle	rectum
43	chr16:31473400-31478800	Strong transcription	Right Ventricle	heart
44	chr16:31473400-31479000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr16:31473400-31479000	Strong transcription	Brain Germinal Matrix	brain
46	chr16:31473400-31479000	Strong transcription	Lung	lung
47	chr16:31473400-31479000	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr16:31473600-31479000	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr16:31473600-31479000	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr16:31473600-31479400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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