Variant report

Variant	rs9939859
Chromosome Location	chr16:31442681-31442682
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF2	chr16:31442580-31442811	GM12878	blood:	n/a	n/a
2	USF1	chr16:31442517-31442902	HCT-116	colon:	n/a	n/a
3	NFYB	chr16:31442564-31442796	GM12878	blood:	n/a	n/a
4	USF1	chr16:31442580-31442830	H1-hESC	embryonic stem cell:	n/a	n/a
5	USF1	chr16:31442596-31442786	H1-hESC	embryonic stem cell:	n/a	n/a
6	USF1	chr16:31442615-31442861	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:31441859..31444739-chr16:31513715..31515828,2	MCF-7	breast:
2	chr16:31104384..31106410-chr16:31441861..31443422,2	MCF-7	breast:
3	chr16:31442416..31446962-chr16:31450558..31455556,7	MCF-7	breast:
4	chr16:30994899..30997136-chr16:31441862..31443740,2	MCF-7	breast:
5	chr16:31440314..31442946-chr16:31447999..31450957,2	K562	blood:
6	chr16:31190516..31192691-chr16:31440671..31443953,3	MCF-7	breast:

No data

Variant related genes	Relation type
COX6A2	TF binding region
ENSG00000167397	Chromatin interaction
ENSG00000099377	Chromatin interaction
ENSG00000089280	Chromatin interaction
ENSG00000176723	Chromatin interaction
ENSG00000255439	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11863224	0.81[ASW][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13332937	1.00[EUR][1000 genomes]
rs13333019	1.00[EUR][1000 genomes]
rs13337777	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2230427	1.00[EUR][1000 genomes]
rs28475579	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28638273	1.00[EUR][1000 genomes]
rs28735967	1.00[EUR][1000 genomes]
rs56032105	1.00[EUR][1000 genomes]
rs58260800	1.00[EUR][1000 genomes]
rs58585879	1.00[EUR][1000 genomes]
rs59137066	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59843953	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7184740	1.00[EUR][1000 genomes]
rs7192438	1.00[EUR][1000 genomes]
rs7194219	0.91[ASW][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7197892	1.00[EUR][1000 genomes]
rs74015528	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74015530	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74015540	1.00[EUR][1000 genomes]
rs8052027	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9925472	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9932709	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059459	chr16:31299088-31462251	Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv542901	chr16:31299088-31462251	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv1066280	chr16:31396464-31452067	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31439200-31447600	Weak transcription	Spleen	Spleen
2	chr16:31439600-31446600	Weak transcription	Esophagus	oesophagus
3	chr16:31439600-31453200	Weak transcription	Lung	lung
4	chr16:31439600-31453800	Weak transcription	Gastric	stomach
5	chr16:31439600-31454000	Weak transcription	Aorta	Aorta
6	chr16:31439800-31443000	Enhancers	Fetal Muscle Leg	muscle
7	chr16:31439800-31443200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr16:31439800-31445000	Weak transcription	Right Atrium	heart
9	chr16:31439800-31446800	Weak transcription	Ovary	ovary
10	chr16:31439800-31447200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr16:31439800-31451600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr16:31439800-31453200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr16:31439800-31453400	Weak transcription	Fetal Brain Female	brain
14	chr16:31440200-31447600	Weak transcription	Pancreas	Pancrea
15	chr16:31440400-31453200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr16:31440600-31451800	Weak transcription	Brain Hippocampus Middle	brain
17	chr16:31440600-31453200	Weak transcription	Liver	Liver
18	chr16:31440800-31443000	Enhancers	Fetal Heart	heart
19	chr16:31441000-31442800	Enhancers	Fetal Intestine Small	intestine
20	chr16:31441000-31443000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr16:31441000-31445400	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr16:31441000-31447600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr16:31441000-31453200	Weak transcription	Brain Anterior Caudate	brain
24	chr16:31441800-31443400	Enhancers	Left Ventricle	heart
25	chr16:31442000-31442800	Enhancers	GM12878-XiMat	blood
26	chr16:31442000-31445000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr16:31442200-31443000	Enhancers	Psoas Muscle	Psoas
28	chr16:31442200-31453800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr16:31442400-31446800	Weak transcription	Fetal Stomach	stomach
30	chr16:31442600-31445000	Weak transcription	Right Ventricle	heart
31	chr16:31442600-31445600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr16:31442600-31446800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr16:31442600-31446800	Weak transcription	Fetal Intestine Large	intestine

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