Variant report

Variant	rs1843050
Chromosome Location	chr3:69403918-69403919
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	GATA3	chr3:69403476-69404582	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr3:69403695-69404709	SK-N-SH	brain:	n/a	n/a
3	GATA2	chr3:69403813-69404525	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
FRMD4B	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1010315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12629224	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12629229	0.90[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12631128	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13061189	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13075664	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13077078	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1483888	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1483889	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1483890	0.98[ASN][1000 genomes]
rs1483891	0.98[ASN][1000 genomes]
rs1564756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1564757	0.82[CHB][hapmap]
rs1843045	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1843046	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1843049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1872152	0.83[MEX][hapmap]
rs2007578	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34184121	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4290808	0.81[CHB][hapmap]
rs4428187	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs6419767	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6549207	0.90[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6549209	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6762186	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6774761	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6774867	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6778232	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6780513	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6783070	0.90[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6807930	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs900669	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs900670	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs900671	0.97[ASN][1000 genomes]
rs9825845	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825849	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861135	1.00[CHB][hapmap];0.82[JPT][hapmap]

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	nsv1007730	chr3:69355932-69730587	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1800315	chr3:69374729-69414587	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv520818	chr3:69401248-69421495	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1843050	FRMD4B	cis	cerebellum	SCAN
rs1843050	FRMD4B	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69397800-69406000	Weak transcription	HSMMtube	muscle
2	chr3:69400200-69405400	Enhancers	Brain Substantia Nigra	brain
3	chr3:69400600-69412800	Weak transcription	Esophagus	oesophagus
4	chr3:69401800-69404000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:69402200-69419000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:69402800-69404200	Enhancers	Brain Anterior Caudate	brain
7	chr3:69402800-69405000	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr3:69402800-69413000	Weak transcription	Aorta	Aorta
9	chr3:69403000-69404000	Enhancers	HSMM	muscle
10	chr3:69403000-69404400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr3:69403000-69404800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:69403000-69405000	Enhancers	Brain Hippocampus Middle	brain
13	chr3:69403000-69406200	Weak transcription	Fetal Thymus	thymus
14	chr3:69403000-69406200	Weak transcription	Left Ventricle	heart
15	chr3:69403000-69414800	Weak transcription	Lung	lung
16	chr3:69403200-69404200	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr3:69403200-69404200	Enhancers	Primary hematopoietic stem cells	blood
18	chr3:69403400-69404400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:69403400-69404400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:69403400-69404600	Weak transcription	Right Atrium	heart
21	chr3:69403400-69404800	Enhancers	Dnd41	blood
22	chr3:69403400-69405000	Enhancers	HUVEC	blood vessel
23	chr3:69403400-69406200	Weak transcription	Fetal Lung	lung
24	chr3:69403800-69404000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:69403800-69404200	Enhancers	Brain Angular Gyrus	brain
26	chr3:69403800-69404400	Enhancers	Brain Germinal Matrix	brain
27	chr3:69403800-69404400	Enhancers	Hela-S3	cervix
28	chr3:69403800-69404600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:69403800-69404800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:69403800-69404800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:69403800-69405000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:69403800-69405000	Enhancers	NHEK	skin
33	chr3:69403800-69406200	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr3:69403800-69406600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr3:69403800-69413000	Weak transcription	Thymus	Thymus

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