Variant report

Variant	rs58863963
Chromosome Location	chr1:184374817-184374818
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	chr1:184374740-184375390	SK-N-SH	brain:	n/a	chr1:184375031-184375039 chr1:184375032-184375048 chr1:184375035-184375043 chr1:184375036-184375043 chr1:184375036-184375043 chr1:184375036-184375043
2	GATA3	chr1:184374766-184375364	MCF-7	breast:	n/a	chr1:184375031-184375039 chr1:184375032-184375048 chr1:184375035-184375043 chr1:184375036-184375043 chr1:184375036-184375043 chr1:184375036-184375043
3	ZNF263	chr1:184374734-184375402	HEK293-T-REx	kidney:	n/a	n/a
4	GATA2	chr1:184374636-184375296	SH-SY5Y	brain:	n/a	chr1:184375031-184375039 chr1:184375032-184375048 chr1:184375036-184375043 chr1:184375036-184375043 chr1:184375036-184375043
5	GATA3	chr1:184374782-184375169	MCF-7	breast:	n/a	chr1:184375031-184375039 chr1:184375032-184375048 chr1:184375035-184375043 chr1:184375036-184375043 chr1:184375036-184375043 chr1:184375036-184375043
6	GATA3	chr1:184374722-184375383	SK-N-SH	brain:	n/a	chr1:184375031-184375039 chr1:184375032-184375048 chr1:184375035-184375043 chr1:184375036-184375043 chr1:184375036-184375043 chr1:184375036-184375043

No.	Distal block	Cell Line	Cell type
1	chr1:184358940..184362912-chr1:184372683..184376846,4	MCF-7	breast:
2	chr1:184373659..184375472-chr1:184386311..184388300,2	MCF-7	breast:
3	chr1:184362934..184364776-chr1:184373656..184376372,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230470	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs16823065	1.00[EUR][1000 genomes]
rs16823118	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823145	0.88[ASN][1000 genomes]
rs2207524	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2378842	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3814334	0.82[AMR][1000 genomes]
rs3922451	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57336256	0.81[ASN][1000 genomes]
rs57590305	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59158738	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59237100	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59598210	0.88[AFR][1000 genomes]
rs60066136	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6424951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6695258	0.85[ASN][1000 genomes]
rs73061677	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73061691	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73063504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73063508	0.88[ASN][1000 genomes]
rs73063512	0.88[ASN][1000 genomes]
rs73063527	0.88[ASN][1000 genomes]
rs7525041	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7540074	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7550032	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184358400-184378200	Weak transcription	Brain Angular Gyrus	brain
2	chr1:184359000-184382800	Weak transcription	Fetal Stomach	stomach
3	chr1:184359400-184377000	Weak transcription	Fetal Intestine Small	intestine
4	chr1:184359600-184377000	Weak transcription	A549	lung
5	chr1:184359600-184391200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr1:184360600-184386200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:184362600-184377000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:184362600-184386200	Weak transcription	Lung	lung
9	chr1:184365000-184378200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:184365200-184376800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:184369000-184375800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:184369000-184377000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:184369000-184377200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:184369200-184376800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:184369200-184377400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:184371800-184378400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr1:184372000-184375200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:184372200-184375200	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:184372200-184376200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr1:184372200-184377000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:184372200-184377800	Weak transcription	Right Atrium	heart
22	chr1:184372200-184382800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:184372400-184375600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:184372400-184376600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:184372400-184377000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:184372400-184377200	Weak transcription	Fetal Heart	heart
27	chr1:184372800-184377400	Weak transcription	Fetal Kidney	kidney
28	chr1:184373000-184379000	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr1:184373400-184376000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:184373600-184375200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:184373600-184376400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:184373800-184375200	Enhancers	Adipose Nuclei	Adipose
33	chr1:184373800-184375800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:184373800-184375800	Enhancers	Fetal Lung	lung
35	chr1:184373800-184376000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:184373800-184378000	Enhancers	Brain Germinal Matrix	brain
37	chr1:184374000-184375000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:184374000-184375000	Enhancers	Psoas Muscle	Psoas
39	chr1:184374000-184377000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:184374200-184375200	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr1:184374200-184375600	Weak transcription	Small Intestine	intestine
42	chr1:184374600-184375400	Enhancers	Fetal Intestine Large	intestine
43	chr1:184374600-184376000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:184374600-184376200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:184374600-184376200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:184374600-184377800	Weak transcription	Ovary	ovary
47	chr1:184374600-184379200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:184374600-184379200	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr1:184374800-184375000	Enhancers	Fetal Brain Male	brain
50	chr1:184374800-184375200	Enhancers	HUES48 Cell Line	embryonic stem cell

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