Variant report

Variant	rs12277924
Chromosome Location	chr11:73219678-73219679
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	POLR2A	chr11:73219533-73219699	MCF-7	breast:	n/a	n/a
2	POLR2A	chr11:73219538-73219699	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000256148	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11235770	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11235809	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11823913	0.91[ASN][1000 genomes]
rs11828904	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12276892	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12285885	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12288753	0.84[AMR][1000 genomes]
rs12290623	0.88[AMR][1000 genomes]
rs12290701	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17132115	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244602	0.82[EUR][1000 genomes]
rs17310361	0.82[EUR][1000 genomes]
rs56857598	0.82[EUR][1000 genomes]
rs57673166	0.82[EUR][1000 genomes]
rs58573166	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59806295	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60860405	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61516411	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7114376	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7115055	0.82[EUR][1000 genomes]
rs7118982	0.84[AMR][1000 genomes]
rs7123985	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7125598	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7129990	0.88[AMR][1000 genomes]
rs7131397	0.81[AFR][1000 genomes]
rs724111	0.82[EUR][1000 genomes]
rs73544783	0.82[EUR][1000 genomes]
rs7927344	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930152	0.82[EUR][1000 genomes]
rs7931767	0.82[EUR][1000 genomes]
rs7933355	0.82[EUR][1000 genomes]
rs7934218	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935948	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938391	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941359	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7944346	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951072	0.82[EUR][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
rs12277924	ARHGEF17	cis	Whole Blood	GTEx

Chromatin state (count:32 , 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	chr11:73212600-73220200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr11:73215600-73232200	Weak transcription	A549	lung
16	chr11:73216600-73223000	Weak transcription	Fetal Brain Male	brain
17	chr11:73217400-73221800	Weak transcription	Brain Hippocampus Middle	brain
18	chr11:73217400-73221800	Weak transcription	Brain Substantia Nigra	brain
19	chr11:73217400-73231400	Weak transcription	Primary T cells from cord blood	blood
20	chr11:73218000-73219800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:73218600-73232600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:73218800-73220000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:73218800-73220200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr11:73218800-73221600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr11:73219000-73231400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr11:73219000-73232200	Weak transcription	Osteobl	bone
27	chr11:73219200-73241400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr11:73219400-73222000	Weak transcription	Lung	lung
29	chr11:73219600-73219800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr11:73219600-73219800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr11:73219600-73220400	ZNF genes & repeats	Brain Germinal Matrix	brain
32	chr11:73219600-73232200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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