Variant report

Variant	rs58682876
Chromosome Location	chr3:116165003-116165004
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	MAZ	chr3:116163676-116165076	IMR90	lung:	n/a	n/a
2	NRF1	chr3:116164892-116165031	H1-hESC	embryonic stem cell:	n/a	n/a
3	SIN3A	chr3:116163671-116165020	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
LSAMP	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs16824895	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55812595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56288785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58653611	1.00[AMR][1000 genomes]
rs73858601	1.00[AMR][1000 genomes]
rs73859213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73859214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73859216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73859217	1.00[AMR][1000 genomes]
rs73861417	1.00[AMR][1000 genomes]
rs73861419	1.00[AMR][1000 genomes]
rs73861420	1.00[AMR][1000 genomes]
rs73861669	1.00[AMR][1000 genomes]
rs73861676	1.00[AMR][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	esv2757886	chr3:116142130-116307542	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2759171	chr3:116142130-116307542	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:116160600-116165200	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr3:116161000-116165200	Active TSS	Brain Substantia Nigra	brain
3	chr3:116163600-116165200	Active TSS	Brain Anterior Caudate	brain
4	chr3:116164200-116169800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:116164400-116165200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:116164400-116165200	Enhancers	Fetal Lung	lung
7	chr3:116164400-116165400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:116164600-116165200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:116164600-116165200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:116164600-116165200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:116164600-116165400	Flanking Active TSS	Brain Cingulate Gyrus	brain
12	chr3:116164800-116165200	Enhancers	H1 Cell Line	embryonic stem cell
13	chr3:116164800-116165200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:116164800-116165200	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr3:116164800-116165400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:116164800-116165400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr3:116164800-116165400	Enhancers	Fetal Stomach	stomach
18	chr3:116164800-116165400	Enhancers	Rectal Smooth Muscle	rectum
19	chr3:116164800-116165600	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr3:116164800-116165600	Enhancers	Colon Smooth Muscle	Colon
21	chr3:116165000-116165200	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr3:116165000-116165200	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr3:116165000-116165200	Enhancers	Brain Germinal Matrix	brain
24	chr3:116165000-116165200	Enhancers	NH-A	brain
25	chr3:116165000-116165400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:116165000-116165400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:116165000-116165400	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr3:116165000-116165400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr3:116165000-116165400	Enhancers	Brain Angular Gyrus	brain
30	chr3:116165000-116165400	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr3:116165000-116165400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:116165000-116165600	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr3:116165000-116165600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:116165000-116167200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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