Variant report

Variant	rs58411583
Chromosome Location	chr1:215744314-215744315
allele	A/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	chr1:215742803-215744458	MCF-7	breast:	n/a	n/a
2	GATA3	chr1:215743611-215744355	SK-N-SH	brain:	n/a	n/a
3	SIN3AK20	chr1:215743682-215744468	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
KCTD3	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs57602690	0.89[AFR][1000 genomes]
rs6695032	0.89[AFR][1000 genomes]
rs73083440	0.89[AFR][1000 genomes]
rs73083442	0.89[AFR][1000 genomes]
rs73083444	0.89[AFR][1000 genomes]
rs73083463	0.89[AFR][1000 genomes]
rs73083482	0.89[AFR][1000 genomes]
rs73083485	0.89[AFR][1000 genomes]
rs73083488	0.89[AFR][1000 genomes]
rs73083502	0.81[AFR][1000 genomes]
rs73085413	0.81[AFR][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	esv1796390	chr1:215561548-215799074	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv430324	chr1:215649163-216082605	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv3334079	chr1:215717606-215745691	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215739800-215744400	Active TSS	NHLF	lung
2	chr1:215740000-215744400	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr1:215741600-215745000	Weak transcription	Gastric	stomach
4	chr1:215741600-215749400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:215741800-215745200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:215741800-215749400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:215741800-215749400	Weak transcription	Lung	lung
8	chr1:215741800-215786200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:215741800-215809800	Weak transcription	Colonic Mucosa	Colon
10	chr1:215742000-215745400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:215742000-215745800	Weak transcription	Right Ventricle	heart
12	chr1:215742000-215746000	Weak transcription	Aorta	Aorta
13	chr1:215742000-215749400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:215742000-215756000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr1:215742000-215786400	Weak transcription	Thymus	Thymus
16	chr1:215742200-215744800	Enhancers	Stomach Mucosa	stomach
17	chr1:215742200-215745400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:215742200-215749600	Weak transcription	Fetal Thymus	thymus
19	chr1:215742200-215767600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:215742200-215786400	Weak transcription	Primary T cells from cord blood	blood
21	chr1:215742400-215744400	Enhancers	Brain Cingulate Gyrus	brain
22	chr1:215742400-215744400	Enhancers	Fetal Heart	heart
23	chr1:215742400-215744600	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr1:215742400-215744600	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr1:215742400-215744800	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr1:215742400-215747400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:215742400-215749400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:215742400-215752600	Weak transcription	HSMMtube	muscle
29	chr1:215742400-215757800	Weak transcription	Dnd41	blood
30	chr1:215742600-215744400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:215742600-215748200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:215742600-215749600	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr1:215742800-215744400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:215742800-215744400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:215742800-215744600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr1:215742800-215744800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:215742800-215744800	Enhancers	HSMM	muscle
38	chr1:215742800-215745000	Enhancers	Fetal Lung	lung
39	chr1:215742800-215745000	Weak transcription	Left Ventricle	heart
40	chr1:215742800-215745000	Weak transcription	Pancreas	Pancrea
41	chr1:215742800-215745800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:215742800-215745800	Weak transcription	Esophagus	oesophagus
43	chr1:215742800-215745800	Weak transcription	Fetal Stomach	stomach
44	chr1:215742800-215746000	Weak transcription	Right Atrium	heart
45	chr1:215742800-215746600	Enhancers	Colon Smooth Muscle	Colon
46	chr1:215742800-215748400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr1:215742800-215749400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:215742800-215749400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr1:215742800-215749400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:215742800-215749400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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