Variant report

Variant	rs11916561
Chromosome Location	chr3:112888977-112888978
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	POLR2A	chr3:112888945-112889009	MCF-7	breast:	n/a	n/a
2	ZNF263	chr3:112888359-112889168	HEK293-T-REx	kidney:	n/a	chr3:112888933-112888954
3	CTCF	chr3:112888860-112889010	GM12873	blood:	n/a	n/a
4	CTCF	chr3:112888840-112888990	GM12864	blood:	n/a	n/a
5	CTCF	chr3:112888920-112889070	GM12875	blood:	n/a	n/a
6	CTCF	chr3:112888840-112888990	HEK293	kidney:	n/a	n/a

Variant related genes	Relation type
ENSG00000243795	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10934225	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1124501	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1124502	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11916474	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632780	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13320844	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1553188	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770031	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6794073	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6794177	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6794383	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7625299	0.86[AFR][1000 genomes]
rs9288974	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9681927	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9868047	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs993703	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer 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	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv517636	chr3:112878536-112893640	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112883800-112889400	Enhancers	Fetal Muscle Leg	muscle
2	chr3:112884000-112889200	Enhancers	Fetal Stomach	stomach
3	chr3:112884000-112889600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:112884000-112889600	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:112884400-112889400	Enhancers	Fetal Lung	lung
6	chr3:112885000-112889200	Enhancers	Fetal Kidney	kidney
7	chr3:112885200-112889000	Enhancers	Placenta Amnion	Placenta Amnion
8	chr3:112885400-112889000	Enhancers	Brain Germinal Matrix	brain
9	chr3:112885400-112889000	Enhancers	Fetal Muscle Trunk	muscle
10	chr3:112886400-112889200	Enhancers	Rectal Smooth Muscle	rectum
11	chr3:112886400-112893600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:112886400-112893800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:112886400-112893800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:112886600-112889200	Enhancers	Stomach Smooth Muscle	stomach
15	chr3:112887000-112889000	Enhancers	Fetal Brain Female	brain
16	chr3:112887800-112889400	Enhancers	Colon Smooth Muscle	Colon
17	chr3:112888000-112889200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:112888000-112889200	Enhancers	Fetal Thymus	thymus
19	chr3:112888200-112889200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr3:112888200-112889400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:112888400-112889000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:112888400-112889000	Enhancers	Fetal Intestine Large	intestine
23	chr3:112888400-112889200	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr3:112888400-112889200	Enhancers	Brain Substantia Nigra	brain
25	chr3:112888400-112889400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:112888800-112889000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:112888800-112889000	Enhancers	Right Atrium	heart
28	chr3:112888800-112889200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:112888800-112889200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:112888800-112889200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:112888800-112889200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
32	chr3:112888800-112889400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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