Variant report

Variant	rs9920459
Chromosome Location	chr15:73458065-73458066
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	SETDB1	chr15:73458065-73458829	U2OS	brain:	n/a	n/a
2	POLR2A	chr15:73458053-73458452	MCF10A-Er-Src	breast:	n/a	n/a
3	GATA1	chr15:73458027-73458762	PBDE	blood:	n/a	n/a

Variant related genes	Relation type
NPM1P43	TF binding region

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1017809	1.00[CEU][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1029	1.00[CEU][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1038136	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11852881	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11853109	1.00[CEU][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11856383	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11856433	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11856466	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11857053	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12101540	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12101734	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13329282	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1382780	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1648248	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1678245	1.00[CEU][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16957661	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1714529	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1714530	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1714532	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1812363	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1842164	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1895842	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1963253	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1963254	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1979410	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2169952	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2254390	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2254818	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2619259	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2623990	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2623994	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2623996	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2624002	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2660823	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2680347	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2680348	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2680350	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2680351	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28547177	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28572029	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28582318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28676873	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28808999	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28828370	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4238459	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4287530	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4325518	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4539561	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4635304	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4776626	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4777584	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs490567	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs492448	0.82[AMR][1000 genomes]
rs514632	0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs524457	1.00[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs533460	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs550212	0.83[YRI][hapmap];0.82[AMR][1000 genomes]
rs55969660	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57453823	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs576414	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6495054	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7176908	1.00[CEU][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7180017	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73438015	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7403367	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7497831	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8031718	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8034243	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8035717	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8038411	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs899480	1.00[CEU][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9920152	1.00[CEU][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9920675	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv517966	chr15:73349633-73488753	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv904339	chr15:73375847-73483718	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv904340	chr15:73375847-73524629	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv904341	chr15:73390790-73483718	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv904342	chr15:73390790-73524629	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv527236	chr15:73421239-73469535	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73401400-73480200	Weak transcription	Right Ventricle	heart
2	chr15:73414400-73458200	Weak transcription	Colonic Mucosa	Colon
3	chr15:73430200-73466600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:73447200-73470000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr15:73448000-73469000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:73449200-73458400	Weak transcription	Fetal Muscle Leg	muscle
7	chr15:73449200-73469000	Weak transcription	Ovary	ovary
8	chr15:73449400-73466600	Weak transcription	Brain Anterior Caudate	brain
9	chr15:73450000-73475400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:73450000-73477400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr15:73452200-73461200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr15:73452200-73470000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:73453200-73458400	Weak transcription	Gastric	stomach
14	chr15:73454600-73458400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr15:73454600-73483000	Weak transcription	Colon Smooth Muscle	Colon
16	chr15:73454800-73466600	Weak transcription	Aorta	Aorta
17	chr15:73454800-73471600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:73455000-73473800	Weak transcription	Fetal Stomach	stomach
19	chr15:73455200-73500400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:73455400-73466600	Weak transcription	Brain Hippocampus Middle	brain
21	chr15:73455400-73466600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:73455800-73460600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr15:73456000-73458200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:73456600-73459000	Strong transcription	Fetal Kidney	kidney
25	chr15:73456600-73459200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:73457000-73458200	Weak transcription	Fetal Intestine Small	intestine
27	chr15:73457000-73459200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:73457400-73458200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:73457400-73458400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:73457400-73459200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
31	chr15:73457400-73461000	Strong transcription	Fetal Intestine Large	intestine
32	chr15:73457600-73459400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:73457600-73470600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr15:73457800-73458200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:73457800-73458200	Weak transcription	Left Ventricle	heart
36	chr15:73457800-73459000	Enhancers	HepG2	liver
37	chr15:73457800-73459200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:73457800-73459200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
39	chr15:73457800-73459200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:73457800-73459200	ZNF genes & repeats	Brain Germinal Matrix	brain
41	chr15:73457800-73459400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
42	chr15:73458000-73458400	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:73458000-73458400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
44	chr15:73458000-73458600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:73458000-73458800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr15:73458000-73458800	Strong transcription	Brain Angular Gyrus	brain
47	chr15:73458000-73458800	ZNF genes & repeats	HMEC	breast
48	chr15:73458000-73458800	Enhancers	NHEK	skin
49	chr15:73458000-73459000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
50	chr15:73458000-73459000	ZNF genes & repeats	Fetal Lung	lung

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