Variant report

Variant	rs55837354
Chromosome Location	chr3:56820833-56820834
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	chr3:56589722..56592080-chr3:56820437..56823322,2	K562	blood:

Variant related genes	Relation type
ENSG00000180376	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10510788	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1110866	0.83[AMR][1000 genomes]
rs11130547	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12054242	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17235733	0.83[AMR][1000 genomes]
rs17288908	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2317250	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2317251	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35550387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55993130	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56122263	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56134339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56201611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57620263	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58478669	0.85[AMR][1000 genomes]
rs60374893	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60882397	0.82[AMR][1000 genomes]
rs62252679	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6795927	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7611544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625636	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7629147	0.86[AMR][1000 genomes]
rs984796	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876818	chr3:56805376-56924711	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55837354	ARHGEF3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56807000-56833200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:56810000-56822200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:56814600-56826800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:56814800-56826600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:56815600-56823400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr3:56815800-56824200	Enhancers	Fetal Heart	heart
7	chr3:56816000-56825400	Enhancers	Primary B cells from peripheral blood	blood
8	chr3:56816200-56827000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr3:56816600-56823200	Enhancers	Brain Germinal Matrix	brain
10	chr3:56817000-56823600	Enhancers	Brain Cingulate Gyrus	brain
11	chr3:56818000-56827000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr3:56818200-56821200	Enhancers	Fetal Brain Male	brain
13	chr3:56818200-56826800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:56818200-56829400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:56818400-56821400	Weak transcription	Adipose Nuclei	Adipose
16	chr3:56818400-56822000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:56818600-56821200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:56818600-56821200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:56818600-56821200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:56818600-56821800	Weak transcription	Fetal Stomach	stomach
21	chr3:56818600-56822200	Weak transcription	Esophagus	oesophagus
22	chr3:56818600-56824000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr3:56818600-56824200	Enhancers	Primary T cells from cord blood	blood
24	chr3:56818600-56826200	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr3:56818600-56829000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:56818600-56832000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:56818800-56821200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr3:56818800-56821400	Weak transcription	Small Intestine	intestine
29	chr3:56818800-56822200	Weak transcription	Colonic Mucosa	Colon
30	chr3:56818800-56822200	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:56818800-56822200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:56818800-56822600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:56819000-56821200	Weak transcription	Fetal Lung	lung
34	chr3:56819000-56829000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr3:56819000-56830400	Weak transcription	HSMM	muscle
36	chr3:56819200-56821200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr3:56819200-56821200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:56819200-56821400	Enhancers	GM12878-XiMat	blood
39	chr3:56819200-56822600	Weak transcription	Stomach Mucosa	stomach
40	chr3:56819200-56824200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr3:56819200-56824400	Weak transcription	Gastric	stomach
42	chr3:56819200-56834400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:56819400-56821200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr3:56819400-56821400	Weak transcription	Primary B cells from cord blood	blood
45	chr3:56819400-56822000	Weak transcription	HSMMtube	muscle
46	chr3:56819400-56822400	Genic enhancers	Fetal Thymus	thymus
47	chr3:56819600-56821000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:56819600-56821200	Weak transcription	Fetal Muscle Leg	muscle
49	chr3:56819600-56821400	Weak transcription	Right Atrium	heart
50	chr3:56819600-56821400	Weak transcription	Right Ventricle	heart

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