Variant report

Variant	rs73544783
Chromosome Location	chr11:73221256-73221257
allele	C/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	USF1	chr11:73221162-73221599	SK-N-SH	brain:	n/a	chr11:73221385-73221394 chr11:73221385-73221394 chr11:73221386-73221395
2	GATA3	chr11:73221163-73221558	SH-SY5Y	brain:	n/a	chr11:73221354-73221364 chr11:73221356-73221363 chr11:73221354-73221363 chr11:73221342-73221363 chr11:73221349-73221370
3	GATA3	chr11:73221032-73221615	SK-N-SH	brain:	n/a	chr11:73221354-73221364 chr11:73221356-73221363 chr11:73221354-73221363 chr11:73221342-73221363 chr11:73221349-73221370
4	GATA2	chr11:73221041-73221552	SH-SY5Y	brain:	n/a	chr11:73221354-73221364 chr11:73221356-73221363 chr11:73221354-73221363 chr11:73221342-73221363 chr11:73221349-73221370
5	EP300	chr11:73220161-73222235	SK-N-SH	brain:	n/a	chr11:73220826-73220840
6	USF1	chr11:73221192-73221619	SK-N-SH_RA	brain:	n/a	chr11:73221385-73221394 chr11:73221385-73221394 chr11:73221386-73221395
7	GATA3	chr11:73221008-73221688	SK-N-SH	brain:	n/a	chr11:73221354-73221364 chr11:73221356-73221363 chr11:73221354-73221363 chr11:73221342-73221363 chr11:73221349-73221370
8	USF1	chr11:73221186-73221516	SK-N-SH_RA	brain:	n/a	chr11:73221385-73221394 chr11:73221385-73221394 chr11:73221386-73221395

Variant related genes	Relation type
ENSG00000256148	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10501411	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11544311	1.00[AMR][1000 genomes]
rs11820577	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11822984	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12099129	0.83[AMR][1000 genomes]
rs12277924	0.82[EUR][1000 genomes]
rs12290785	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244596	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17244602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244616	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17310361	1.00[EUR][1000 genomes]
rs17310374	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56742470	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56857598	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56884659	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57491850	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57673166	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58334887	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58564192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60924672	0.83[AMR][1000 genomes]
rs61345051	0.83[AMR][1000 genomes]
rs6592526	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101561	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7110369	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7114376	0.80[EUR][1000 genomes]
rs7115055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129546	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724111	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542938	0.92[AMR][1000 genomes]
rs73542952	0.83[AMR][1000 genomes]
rs73542960	0.83[AMR][1000 genomes]
rs73542967	0.83[AMR][1000 genomes]
rs73542976	0.83[AMR][1000 genomes]
rs73542979	0.83[AMR][1000 genomes]
rs73543000	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73544710	1.00[ASN][1000 genomes]
rs73544711	1.00[ASN][1000 genomes]
rs73544716	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73544720	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73544729	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73544767	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73546720	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73546735	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548680	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548688	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548693	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73550316	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7925226	0.83[AMR][1000 genomes]
rs7930152	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930907	0.88[AFR][1000 genomes]
rs7931767	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7933355	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935948	0.82[EUR][1000 genomes]
rs7938391	0.82[EUR][1000 genomes]
rs7944346	0.82[EUR][1000 genomes]
rs7945825	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7950375	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951072	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv508641	chr11:73149281-73235528	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv520130	chr11:73183598-73223776	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv1048171	chr11:73210060-73271831	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs73544783	ARHGEF17	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73141800-73231600	Weak transcription	Thymus	Thymus
2	chr11:73163800-73225600	Weak transcription	Fetal Stomach	stomach
3	chr11:73182000-73230000	Weak transcription	Dnd41	blood
4	chr11:73202400-73240000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:73205000-73239600	Weak transcription	Primary B cells from cord blood	blood
6	chr11:73205600-73236400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr11:73205800-73241400	Weak transcription	Pancreas	Pancrea
8	chr11:73206000-73222000	Weak transcription	Left Ventricle	heart
9	chr11:73206200-73224600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:73206200-73232600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:73207600-73225600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr11:73209400-73221600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr11:73210200-73231400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr11:73215600-73232200	Weak transcription	A549	lung
15	chr11:73216600-73223000	Weak transcription	Fetal Brain Male	brain
16	chr11:73217400-73221800	Weak transcription	Brain Hippocampus Middle	brain
17	chr11:73217400-73221800	Weak transcription	Brain Substantia Nigra	brain
18	chr11:73217400-73231400	Weak transcription	Primary T cells from cord blood	blood
19	chr11:73218600-73232600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:73218800-73221600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:73219000-73231400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr11:73219000-73232200	Weak transcription	Osteobl	bone
23	chr11:73219200-73241400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr11:73219400-73222000	Weak transcription	Lung	lung
25	chr11:73219600-73232200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr11:73219800-73230400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr11:73220000-73232200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr11:73220400-73231800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr11:73220400-73231800	Weak transcription	Brain Germinal Matrix	brain
30	chr11:73221000-73221800	Enhancers	Liver	Liver
31	chr11:73221000-73221800	Enhancers	Brain Anterior Caudate	brain
32	chr11:73221000-73225600	Weak transcription	HepG2	liver
33	chr11:73221200-73222200	Enhancers	Brain Angular Gyrus	brain
34	chr11:73221200-73222400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr11:73221200-73238000	Weak transcription	Psoas Muscle	Psoas

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