Variant report

Variant	rs10513826
Chromosome Location	chr3:116164892-116164893
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	CTBP2	chr3:116163661-116164948	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAZ	chr3:116163676-116165076	IMR90	lung:	n/a	n/a
3	POLR2A	chr3:116162922-116164945	SK-N-MC	brain:	n/a	n/a
4	NRF1	chr3:116164892-116165031	H1-hESC	embryonic stem cell:	n/a	n/a
5	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: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11924642	0.81[CHD][hapmap]
rs11928524	0.81[CHD][hapmap]
rs13069948	0.86[CHD][hapmap]
rs13070962	0.80[CHD][hapmap]
rs13092244	0.86[TSI][hapmap]
rs13316464	0.90[CEU][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap]
rs13323946	0.81[CHD][hapmap]
rs1367770	0.81[CHD][hapmap]
rs16824908	0.89[CEU][hapmap];0.87[CHD][hapmap]
rs1731596	0.86[CHD][hapmap]
rs17647091	0.80[CHD][hapmap]
rs1920175	0.90[CEU][hapmap]
rs41442746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap]
rs4831097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4831133	0.86[CHD][hapmap]
rs4831136	0.86[CHD][hapmap]
rs67644980	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6767942	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6777473	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7634137	0.81[CHD][hapmap]
rs7637573	0.86[CHD][hapmap]
rs7638540	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7652923	0.85[CHD][hapmap]
rs9289050	0.86[CHD][hapmap]
rs9838534	0.85[CHD][hapmap]
rs9857124	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9875727	0.89[CEU][hapmap];0.86[JPT][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10513826	GTF2E1	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:116160400-116165000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:116160600-116165200	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr3:116161000-116165200	Active TSS	Brain Substantia Nigra	brain
4	chr3:116163600-116165200	Active TSS	Brain Anterior Caudate	brain
5	chr3:116164200-116169800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:116164400-116165000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:116164400-116165000	Enhancers	Fetal Muscle Leg	muscle
8	chr3:116164400-116165200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:116164400-116165200	Enhancers	Fetal Lung	lung
10	chr3:116164400-116165400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:116164600-116165000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:116164600-116165000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:116164600-116165000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr3:116164600-116165000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr3:116164600-116165000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:116164600-116165000	Flanking Active TSS	Brain Angular Gyrus	brain
17	chr3:116164600-116165000	Flanking Active TSS	Brain Germinal Matrix	brain
18	chr3:116164600-116165000	Flanking Active TSS	Fetal Brain Male	brain
19	chr3:116164600-116165200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:116164600-116165200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:116164600-116165200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:116164600-116165400	Flanking Active TSS	Brain Cingulate Gyrus	brain
23	chr3:116164800-116165000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr3:116164800-116165000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr3:116164800-116165000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr3:116164800-116165000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr3:116164800-116165000	Active TSS	Brain Hippocampus Middle	brain
28	chr3:116164800-116165000	Enhancers	Fetal Brain Female	brain
29	chr3:116164800-116165000	Enhancers	Stomach Smooth Muscle	stomach
30	chr3:116164800-116165000	Enhancers	HSMMtube	muscle
31	chr3:116164800-116165200	Enhancers	H1 Cell Line	embryonic stem cell
32	chr3:116164800-116165200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:116164800-116165200	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr3:116164800-116165400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:116164800-116165400	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr3:116164800-116165400	Enhancers	Fetal Stomach	stomach
37	chr3:116164800-116165400	Enhancers	Rectal Smooth Muscle	rectum
38	chr3:116164800-116165600	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr3:116164800-116165600	Enhancers	Colon Smooth Muscle	Colon

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