Variant report

Variant	rs73548688
Chromosome Location	chr11:73279544-73279545
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	chr11:73275181..73277869-chr11:73279088..73282119,3	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10501411	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235809	0.80[EUR][1000 genomes]
rs11544311	0.83[AMR][1000 genomes]
rs11820577	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11822984	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12285885	0.80[EUR][1000 genomes]
rs12290701	0.82[EUR][1000 genomes]
rs12290785	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17132115	0.82[EUR][1000 genomes]
rs17244596	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17244602	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244616	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17310361	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17310374	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56742470	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56857598	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56884659	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57491850	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57673166	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58334887	1.00[ASN][1000 genomes]
rs58564192	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58573166	0.82[EUR][1000 genomes]
rs59806295	0.80[EUR][1000 genomes]
rs60860405	0.82[EUR][1000 genomes]
rs61516411	0.80[EUR][1000 genomes]
rs6592526	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101561	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7110369	1.00[ASN][1000 genomes]
rs7115055	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7118057	0.83[AFR][1000 genomes]
rs7123985	0.82[EUR][1000 genomes]
rs7129546	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724111	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73543000	1.00[ASN][1000 genomes]
rs73544710	1.00[ASN][1000 genomes]
rs73544711	1.00[ASN][1000 genomes]
rs73544716	1.00[ASN][1000 genomes]
rs73544720	1.00[ASN][1000 genomes]
rs73544729	1.00[ASN][1000 genomes]
rs73544767	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73544783	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73546720	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73546735	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548680	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548693	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73550316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930152	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930907	0.92[AFR][1000 genomes]
rs7931767	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7933355	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7943721	0.83[AFR][1000 genomes]
rs7945825	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7950375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951072	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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	nsv983188	chr11:73273934-73307064	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs73548688	ARHGEF17	cis	Whole Blood	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73243400-73279600	Weak transcription	Fetal Stomach	stomach
2	chr11:73250000-73307800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr11:73250800-73282800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr11:73251000-73288800	Weak transcription	Thymus	Thymus
5	chr11:73253800-73307000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr11:73262200-73281000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr11:73263200-73306000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr11:73263800-73288800	Weak transcription	Colon Smooth Muscle	Colon
9	chr11:73264600-73287000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr11:73265400-73287200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr11:73266400-73280000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:73266600-73307800	Weak transcription	Fetal Intestine Small	intestine
13	chr11:73267400-73281400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr11:73267400-73284800	Weak transcription	Right Atrium	heart
15	chr11:73268400-73281000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:73269800-73279600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:73270600-73288000	Weak transcription	NHLF	lung
18	chr11:73272200-73307600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr11:73274600-73287000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr11:73274600-73287000	Weak transcription	Brain Substantia Nigra	brain
21	chr11:73274800-73290800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr11:73275200-73286800	Weak transcription	Brain Anterior Caudate	brain
23	chr11:73275200-73287000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr11:73275400-73284600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:73275400-73288800	Weak transcription	GM12878-XiMat	blood
26	chr11:73275400-73307000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr11:73276200-73287200	Weak transcription	Brain Angular Gyrus	brain
28	chr11:73276400-73287400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:73276400-73289800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:73276400-73296800	Weak transcription	Fetal Muscle Leg	muscle
31	chr11:73276400-73299200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr11:73276400-73307000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr11:73276600-73286800	Weak transcription	Fetal Brain Female	brain
34	chr11:73277000-73279600	Strong transcription	Primary T cells from cord blood	blood
35	chr11:73277000-73281200	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr11:73277200-73285800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr11:73277200-73299600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr11:73277400-73279800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:73277400-73280600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr11:73277400-73281600	Weak transcription	HSMM	muscle
41	chr11:73277400-73307800	Weak transcription	Fetal Intestine Large	intestine
42	chr11:73277600-73280200	Weak transcription	HMEC	breast
43	chr11:73277600-73281000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr11:73277600-73286800	Weak transcription	Brain Germinal Matrix	brain
45	chr11:73277600-73287200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr11:73277600-73293800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr11:73278000-73280600	Strong transcription	Primary B cells from cord blood	blood
48	chr11:73278000-73281200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr11:73278000-73281200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr11:73278000-73288000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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