Variant report

Variant	rs12492305
Chromosome Location	chr3:118953691-118953692
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	GATA3	chr3:118953561-118954453	SK-N-SH	brain:	n/a	chr3:118953692-118953702 chr3:118954083-118954093

No.	Distal block	Cell Line	Cell type
1	chr3:118943947..118945646-chr3:118952153..118954187,2	K562	blood:
2	chr3:118946339..118949651-chr3:118951974..118954815,3	MCF-7	breast:
3	chr3:118952753..118957545-chr3:118958102..118959880,7	K562	blood:

Variant related genes	Relation type
B4GALT4	TF binding region
ENSG00000240254	Chromatin interaction
ENSG00000121578	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12487052	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13315549	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13320556	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16829413	0.83[ASN][1000 genomes]
rs2594731	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28428903	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4234656	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67108505	0.81[ASN][1000 genomes]
rs6766503	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6774	0.87[ASN][1000 genomes]
rs6805930	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9844248	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118924400-118959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:118927000-118953800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:118927000-118953800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:118927200-118953800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:118927200-118955200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr3:118927800-118956400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:118928000-118955600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:118929200-118956200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:118929200-118956200	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:118929200-118956400	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr3:118929200-118956600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:118930000-118955400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr3:118930200-118955800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:118930200-118958400	Weak transcription	Hela-S3	cervix
15	chr3:118931600-118957400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:118932600-118955800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:118944000-118954800	Strong transcription	Fetal Stomach	stomach
18	chr3:118944400-118954000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:118944400-118955800	Strong transcription	Placenta	Placenta
20	chr3:118944400-118956200	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:118944800-118954600	Strong transcription	Primary hematopoietic stem cells	blood
22	chr3:118944800-118955000	Strong transcription	Primary B cells from cord blood	blood
23	chr3:118944800-118955000	Strong transcription	Fetal Lung	lung
24	chr3:118944800-118955600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:118945000-118956000	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr3:118945000-118956000	Strong transcription	Liver	Liver
27	chr3:118945800-118958600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:118946200-118953800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:118946600-118957800	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:118946800-118957200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:118947200-118955200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr3:118947400-118953800	Strong transcription	Duodenum Mucosa	Duodenum
33	chr3:118947400-118955800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:118948200-118954200	Weak transcription	Aorta	Aorta
35	chr3:118948200-118954200	Weak transcription	Stomach Mucosa	stomach
36	chr3:118948200-118955600	Weak transcription	Psoas Muscle	Psoas
37	chr3:118948200-118956200	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr3:118948400-118958600	Weak transcription	Colonic Mucosa	Colon
39	chr3:118949000-118954000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr3:118949000-118958000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:118949000-118958400	Weak transcription	Fetal Brain Male	brain
42	chr3:118949200-118957600	Weak transcription	Fetal Heart	heart
43	chr3:118949400-118954200	Weak transcription	Fetal Kidney	kidney
44	chr3:118949400-118957600	Weak transcription	Right Ventricle	heart
45	chr3:118949400-118958800	Weak transcription	Lung	lung
46	chr3:118949600-118954200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr3:118949600-118955800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
48	chr3:118949600-118957600	Weak transcription	Ovary	ovary
49	chr3:118949600-118958400	Weak transcription	Brain Substantia Nigra	brain
50	chr3:118949600-118958600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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