Variant report

Variant	rs12489969
Chromosome Location	chr3:177400888-177400889
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	EBF1	chr3:177400877-177400982	GM12878	blood:	n/a	chr3:177400880-177400889 chr3:177400879-177400889 chr3:177400879-177400890 chr3:177400878-177400891 chr3:177400880-177400889

Variant related genes	Relation type
ENSG00000228561	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10513747	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10513749	0.84[ASN][1000 genomes]
rs10513750	0.82[ASN][1000 genomes]
rs10936953	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11915692	0.95[ASN][1000 genomes]
rs12487312	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12487458	0.83[ASN][1000 genomes]
rs12489304	0.82[ASN][1000 genomes]
rs12496321	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13059514	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13060224	0.83[ASN][1000 genomes]
rs13060502	0.83[ASN][1000 genomes]
rs13064192	0.84[ASN][1000 genomes]
rs13071785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13074455	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13082519	0.83[ASN][1000 genomes]
rs13097562	0.85[ASN][1000 genomes]
rs13098037	0.85[ASN][1000 genomes]
rs13340118	0.83[ASN][1000 genomes]
rs13340167	0.83[ASN][1000 genomes]
rs13340172	0.83[ASN][1000 genomes]
rs1499809	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1499811	0.87[ASN][1000 genomes]
rs1500048	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17635512	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17635597	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2062499	0.82[ASN][1000 genomes]
rs2062500	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33964414	0.82[ASN][1000 genomes]
rs34066617	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34347103	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34407557	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34491022	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34557886	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34638059	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34763113	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35110045	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35468531	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35610650	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35652846	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35791913	0.82[ASN][1000 genomes]
rs35830472	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35847814	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35868955	0.82[ASN][1000 genomes]
rs36055300	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56005554	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57405296	0.83[ASN][1000 genomes]
rs61541774	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62283347	0.81[ASN][1000 genomes]
rs66636257	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67189039	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67797381	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6793629	0.83[ASN][1000 genomes]
rs68151580	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71308158	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7610506	0.82[ASN][1000 genomes]
rs7639373	0.82[ASN][1000 genomes]
rs7641099	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752972	chr3:176924298-177425298	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv931055	chr3:177229521-177889872	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:177392000-177405400	Weak transcription	Brain Substantia Nigra	brain
2	chr3:177392200-177404400	Weak transcription	Ovary	ovary
3	chr3:177392400-177418800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:177394000-177401000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:177394800-177404800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:177395000-177406000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:177395000-177411600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:177396000-177401000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr3:177396000-177401200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:177398000-177401200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:177398000-177401400	Weak transcription	Adipose Nuclei	Adipose
12	chr3:177398000-177401800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:177398000-177402000	Enhancers	HUVEC	blood vessel
14	chr3:177398800-177405200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:177398800-177421600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:177399400-177401800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:177399400-177402000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:177399600-177401000	Enhancers	Spleen	Spleen
19	chr3:177399600-177401800	Enhancers	Primary T cells fromperipheralblood	blood
20	chr3:177399600-177402000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr3:177399800-177401000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:177400000-177402000	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr3:177400200-177401000	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr3:177400200-177401000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr3:177400200-177401600	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr3:177400200-177401600	Enhancers	Dnd41	blood
27	chr3:177400400-177406200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:177400600-177401400	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:177400600-177401800	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr3:177400800-177401000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr3:177400800-177401000	Enhancers	Left Ventricle	heart

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