Variant report

Variant	rs56884659
Chromosome Location	chr11:73252947-73252948
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:73252164..73254240-chr11:73308576..73310454,2	K562	blood:

Variant related genes	Relation type
ENSG00000054965	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

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	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17244602	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244616	0.87[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56742470	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56857598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57491850	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57673166	1.00[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	1.00[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	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101561	0.88[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	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7123985	0.82[EUR][1000 genomes]
rs7129546	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724111	1.00[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	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73544767	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73544783	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73546720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73546735	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548688	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548693	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73550316	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930907	0.88[AFR][1000 genomes]
rs7931767	1.00[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]
rs7945825	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7950375	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951072	1.00[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	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
rs56884659	ARHGEF17	cis	Whole Blood	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73240400-73253800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:73240400-73254400	Weak transcription	Stomach Mucosa	stomach
3	chr11:73240600-73255400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr11:73243400-73279600	Weak transcription	Fetal Stomach	stomach
5	chr11:73243800-73263000	Weak transcription	Fetal Intestine Small	intestine
6	chr11:73244000-73253000	Weak transcription	Psoas Muscle	Psoas
7	chr11:73246200-73256400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr11:73249400-73253400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr11:73249600-73253800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:73249600-73266000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr11:73249600-73266400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr11:73249600-73276000	Weak transcription	Fetal Muscle Leg	muscle
13	chr11:73249800-73253000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr11:73249800-73253000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr11:73249800-73253400	Weak transcription	Small Intestine	intestine
16	chr11:73249800-73262600	Weak transcription	Brain Anterior Caudate	brain
17	chr11:73250000-73253400	Weak transcription	Fetal Heart	heart
18	chr11:73250000-73255000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:73250000-73255200	Weak transcription	HSMM	muscle
20	chr11:73250000-73261800	Weak transcription	Brain Substantia Nigra	brain
21	chr11:73250000-73262200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr11:73250000-73262600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr11:73250000-73262600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr11:73250000-73262800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:73250000-73265800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr11:73250000-73307800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr11:73250200-73253200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:73250200-73266400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr11:73250200-73278800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr11:73250800-73253400	Weak transcription	Brain Angular Gyrus	brain
31	chr11:73250800-73262200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr11:73250800-73265800	Weak transcription	Right Atrium	heart
33	chr11:73250800-73282800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr11:73251000-73253000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr11:73251000-73253200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:73251000-73255200	Weak transcription	GM12878-XiMat	blood
37	chr11:73251000-73265600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:73251000-73288800	Weak transcription	Thymus	Thymus
39	chr11:73251200-73258600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr11:73251200-73263000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr11:73251600-73255200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr11:73251600-73262200	Weak transcription	Right Ventricle	heart
43	chr11:73251600-73262400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr11:73251600-73266000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:73251800-73253200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr11:73251800-73253600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr11:73252000-73254000	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr11:73252000-73258000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr11:73252000-73261200	Weak transcription	Dnd41	blood
50	chr11:73252200-73253000	Weak transcription	Ovary	ovary

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