Variant report

Variant	rs72804140
Chromosome Location	chr16:75340938-75340939
allele	C/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	SP1	chr16:75338303-75341123	HCT-116	colon:	n/a	chr16:75338460-75338469 chr16:75338514-75338535 chr16:75338711-75338725
2	JUN	chr16:75339068-75340944	HepG2	liver:	n/a	chr16:75340845-75340852 chr16:75339585-75339595 chr16:75339582-75339593 chr16:75339585-75339595 chr16:75339586-75339594 chr16:75339585-75339595
3	RCOR1	chr16:75340857-75341003	HepG2	liver:	n/a	n/a
4	SP1	chr16:75338485-75340949	HCT-116	colon:	n/a	chr16:75338514-75338535 chr16:75338711-75338725
5	FOSL1	chr16:75338510-75341143	HCT-116	colon:	n/a	chr16:75340845-75340852 chr16:75339585-75339595 chr16:75339582-75339593 chr16:75339584-75339595 chr16:75339585-75339595 chr16:75339586-75339594 chr16:75339585-75339595
6	POLR2A	chr16:75338289-75340987	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:75282402..75286042-chr16:75337577..75341093,9	MCF-7	breast:
2	chr16:75282912..75287259-chr16:75337955..75341068,4	MCF-7	breast:
3	chr16:75282975..75286210-chr16:75340217..75342691,3	K562	blood:
4	chr16:75298649..75302173-chr16:75337597..75342572,10	MCF-7	breast:

Variant related genes	Relation type
CFDP1	TF binding region
ENSG00000050820	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs17605723	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17605814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17606084	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17674257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs187435	0.87[EUR][1000 genomes]
rs2454860	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs247429	0.87[EUR][1000 genomes]
rs247441	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs37590	0.84[EUR][1000 genomes]
rs391192	0.90[EUR][1000 genomes]
rs4243113	0.90[EUR][1000 genomes]
rs469176	0.87[EUR][1000 genomes]
rs58518445	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6564246	0.97[EUR][1000 genomes]
rs66885758	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66886787	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67836283	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7185976	0.90[EUR][1000 genomes]
rs7192448	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7193299	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7199718	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7202997	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72787117	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72787126	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72787129	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72787135	0.90[EUR][1000 genomes]
rs72787147	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs72787159	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs72787163	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72787169	0.84[EUR][1000 genomes]
rs72804118	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72804120	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72804135	0.99[EUR][1000 genomes]
rs72804141	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72804154	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72804155	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72804160	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72804161	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72804162	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8044442	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8055093	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	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
6	nsv833283	chr16:75302175-75392308	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75317400-75358000	Weak transcription	Fetal Brain Male	brain
2	chr16:75332600-75352000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:75335000-75346400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr16:75336000-75346600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr16:75336600-75343000	Weak transcription	Gastric	stomach
6	chr16:75336800-75346600	Weak transcription	Ovary	ovary
7	chr16:75338000-75341000	Enhancers	NHLF	lung
8	chr16:75338000-75342200	Enhancers	Brain Hippocampus Middle	brain
9	chr16:75338200-75341000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr16:75338200-75341000	Enhancers	Brain Substantia Nigra	brain
11	chr16:75338200-75341000	Enhancers	Right Atrium	heart
12	chr16:75338200-75341000	Enhancers	NH-A	brain
13	chr16:75338200-75341200	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr16:75338400-75342200	Enhancers	Brain Angular Gyrus	brain
15	chr16:75338800-75341000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr16:75338800-75341000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr16:75338800-75341000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr16:75338800-75341000	Enhancers	Brain Cingulate Gyrus	brain
19	chr16:75338800-75341000	Flanking Active TSS	HepG2	liver
20	chr16:75338800-75343000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr16:75338800-75346600	Weak transcription	Fetal Brain Female	brain
22	chr16:75338800-75349400	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr16:75338800-75349800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr16:75338800-75351200	Weak transcription	Right Ventricle	heart
25	chr16:75338800-75426400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr16:75339000-75341000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr16:75339000-75341000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr16:75339000-75341000	Enhancers	HSMM	muscle
29	chr16:75339000-75341400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr16:75339000-75342200	Enhancers	Placenta	Placenta
31	chr16:75339000-75346800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr16:75339000-75347000	Weak transcription	Lung	lung
33	chr16:75339200-75341000	Enhancers	Colonic Mucosa	Colon
34	chr16:75339200-75358000	Weak transcription	Brain Germinal Matrix	brain
35	chr16:75339400-75341000	Enhancers	Brain Anterior Caudate	brain
36	chr16:75339400-75342800	Enhancers	K562	blood
37	chr16:75339400-75411800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr16:75339600-75341000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
39	chr16:75339600-75341000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr16:75339600-75341800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr16:75339600-75342200	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr16:75339600-75343400	Weak transcription	Primary B cells from cord blood	blood
43	chr16:75339600-75343400	Enhancers	Fetal Muscle Leg	muscle
44	chr16:75339800-75341000	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr16:75339800-75341000	Flanking Active TSS	A549	lung
46	chr16:75339800-75342400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr16:75339800-75346800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr16:75339800-75347000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr16:75339800-75347000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr16:75340000-75341000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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