Variant report

Variant	rs73542990
Chromosome Location	chr11:73134398-73134399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:73129898..73132865-chr11:73133387..73134991,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1002127	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11544310	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11544311	1.00[EUR][1000 genomes]
rs12099129	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12288753	0.84[EUR][1000 genomes]
rs12290623	0.83[EUR][1000 genomes]
rs17244596	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17851510	0.87[EUR][1000 genomes]
rs1938777	0.80[EUR][1000 genomes]
rs2298469	0.84[EUR][1000 genomes]
rs28400367	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56742470	0.91[AMR][1000 genomes]
rs57354084	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58334887	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60924672	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61345051	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6592526	1.00[AMR][1000 genomes]
rs7110369	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7112924	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114009	0.83[EUR][1000 genomes]
rs7118982	0.84[EUR][1000 genomes]
rs7129546	0.91[AMR][1000 genomes]
rs7129990	0.83[EUR][1000 genomes]
rs73542929	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542938	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542952	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542960	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542967	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542976	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542979	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73543000	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73544710	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73544711	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73544716	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73544720	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73544729	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73544767	1.00[AMR][1000 genomes]
rs7925226	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941454	0.82[EUR][1000 genomes]
rs7951174	0.90[EUR][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs73542990	ARHGEF17	cis	Whole Blood	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73099200-73139800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr11:73099200-73141000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr11:73115200-73149400	Weak transcription	Fetal Kidney	kidney
4	chr11:73118800-73137600	Weak transcription	Colonic Mucosa	Colon
5	chr11:73120800-73140600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:73120800-73141200	Weak transcription	Esophagus	oesophagus
7	chr11:73120800-73149000	Weak transcription	Fetal Lung	lung
8	chr11:73120800-73149800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr11:73120800-73150000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr11:73121000-73150200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:73122400-73134400	Weak transcription	NHEK	skin
12	chr11:73122400-73163200	Weak transcription	Aorta	Aorta
13	chr11:73122600-73134400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:73122800-73139000	Weak transcription	Spleen	Spleen
15	chr11:73122800-73149600	Weak transcription	Gastric	stomach
16	chr11:73123800-73209600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:73124000-73140800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr11:73126600-73137400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr11:73126600-73149400	Weak transcription	Small Intestine	intestine
20	chr11:73126800-73137200	Weak transcription	Colon Smooth Muscle	Colon
21	chr11:73127800-73136600	Weak transcription	Brain Angular Gyrus	brain
22	chr11:73127800-73137000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr11:73127800-73137400	Weak transcription	Right Ventricle	heart
24	chr11:73128000-73137400	Weak transcription	Psoas Muscle	Psoas
25	chr11:73128200-73137400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:73128400-73135800	Weak transcription	Brain Substantia Nigra	brain
27	chr11:73128400-73136800	Weak transcription	HSMM	muscle
28	chr11:73128400-73137200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr11:73128400-73137400	Weak transcription	NH-A	brain
30	chr11:73128600-73137200	Weak transcription	NHLF	lung
31	chr11:73128600-73139400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr11:73128600-73139400	Weak transcription	NHDF-Ad	bronchial
33	chr11:73129200-73137400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:73129400-73152400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr11:73129600-73136200	Weak transcription	GM12878-XiMat	blood
36	chr11:73129600-73140000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr11:73129600-73147000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr11:73129600-73149400	Weak transcription	Liver	Liver
39	chr11:73129600-73150000	Weak transcription	Fetal Intestine Small	intestine
40	chr11:73129800-73134400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:73129800-73141200	Weak transcription	Fetal Brain Male	brain
42	chr11:73130400-73141200	Weak transcription	Pancreas	Pancrea
43	chr11:73130600-73139200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr11:73130600-73139400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr11:73130600-73141000	Weak transcription	Thymus	Thymus
46	chr11:73130800-73135600	Weak transcription	Placenta	Placenta
47	chr11:73130800-73135800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr11:73130800-73140000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr11:73130800-73140400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr11:73130800-73150000	Weak transcription	Duodenum Mucosa	Duodenum

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