Variant report

Variant	rs10926624
Chromosome Location	chr1:242310046-242310047
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	chr1:242310018-242311022	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr1:242310027-242310823	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:242309993-242311065	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr1:242309905-242310928	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000272865	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10803017	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10803018	0.87[EUR][1000 genomes]
rs11582266	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11587429	0.84[EUR][1000 genomes]
rs12088502	0.86[MEX][hapmap]
rs1550125	0.88[CEU][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs28847350	0.83[EUR][1000 genomes]
rs4658425	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4658657	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59012281	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66533138	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6673243	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs737133	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7534695	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7535289	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7538792	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs934622	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv948409	chr1:241830086-242489705	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	esv2750831	chr1:242025098-242332959	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv468672	chr1:242201247-242555949	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv470788	chr1:242201247-242555949	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv549462	chr1:242201247-242555949	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv528016	chr1:242223399-242451350	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv549463	chr1:242265419-242856854	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv998804	chr1:242281003-242491362	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv430391	chr1:242307104-243280885	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10926624	AKT3	cis	parietal	SCAN
rs10926624	FMN2	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:242299000-242310400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:242303400-242310400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr1:242307800-242310400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:242309400-242310800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr1:242309400-242311000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:242309600-242310400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:242309800-242310200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:242309800-242310800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:242309800-242311000	Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr1:242309800-242311200	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr1:242310000-242310200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:242310000-242310200	Active TSS	Brain Angular Gyrus	brain
13	chr1:242310000-242310200	Flanking Active TSS	Dnd41	blood
14	chr1:242310000-242310200	Flanking Active TSS	GM12878-XiMat	blood
15	chr1:242310000-242310400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
16	chr1:242310000-242310400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:242310000-242310400	Active TSS	Brain Anterior Caudate	brain
18	chr1:242310000-242310400	Active TSS	Brain Cingulate Gyrus	brain
19	chr1:242310000-242310400	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr1:242310000-242310400	Active TSS	NH-A	brain
21	chr1:242310000-242310600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:242310000-242310600	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr1:242310000-242310600	Active TSS	Fetal Brain Female	brain
24	chr1:242310000-242310600	Flanking Active TSS	Fetal Lung	lung
25	chr1:242310000-242310600	Active TSS	Monocytes-CD14+_RO01746	blood
26	chr1:242310000-242310800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:242310000-242310800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:242310000-242310800	Active TSS	Muscle Satellite Cultured Cells	--
29	chr1:242310000-242310800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:242310000-242310800	Active TSS	Adipose Nuclei	Adipose
31	chr1:242310000-242310800	Active TSS	Ovary	ovary
32	chr1:242310000-242310800	Active TSS	A549	lung
33	chr1:242310000-242311000	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr1:242310000-242311000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:242310000-242311000	Enhancers	HMEC	breast

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