Variant report

Variant	rs55993130
Chromosome Location	chr3:56820192-56820193
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:56817895..56820572-chr3:56821053..56822921,2	K562	blood:
2	chr3:56817648..56820572-chr3:56821053..56824731,3	K562	blood:

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

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

rs_ID	r²[population]
rs10510788	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1110866	0.84[AMR][1000 genomes]
rs11130547	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12054242	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17235733	0.84[AMR][1000 genomes]
rs17288908	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2317250	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2317251	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35550387	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55837354	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56122263	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56134339	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56201611	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57620263	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58478669	0.88[AMR][1000 genomes]
rs60374893	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60882397	0.86[AMR][1000 genomes]
rs62252679	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6795927	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7611544	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7625636	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7629147	0.83[AMR][1000 genomes]
rs984796	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][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
rs55993130	ARHGEF3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 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	chr3:56815400-56820200	Enhancers	Psoas Muscle	Psoas
6	chr3:56815600-56820800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:56815600-56823400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr3:56815800-56820200	Enhancers	Left Ventricle	heart
9	chr3:56815800-56820800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:56815800-56824200	Enhancers	Fetal Heart	heart
11	chr3:56816000-56825400	Enhancers	Primary B cells from peripheral blood	blood
12	chr3:56816200-56820800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:56816200-56827000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr3:56816600-56823200	Enhancers	Brain Germinal Matrix	brain
15	chr3:56817000-56823600	Enhancers	Brain Cingulate Gyrus	brain
16	chr3:56817600-56820800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:56817800-56820200	Enhancers	Pancreas	Pancrea
18	chr3:56818000-56827000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr3:56818200-56821200	Enhancers	Fetal Brain Male	brain
20	chr3:56818200-56826800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:56818200-56829400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:56818400-56820200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
23	chr3:56818400-56820200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:56818400-56821400	Weak transcription	Adipose Nuclei	Adipose
25	chr3:56818400-56822000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:56818600-56821200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:56818600-56821200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:56818600-56821200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:56818600-56821800	Weak transcription	Fetal Stomach	stomach
30	chr3:56818600-56822200	Weak transcription	Esophagus	oesophagus
31	chr3:56818600-56824000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr3:56818600-56824200	Enhancers	Primary T cells from cord blood	blood
33	chr3:56818600-56826200	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr3:56818600-56829000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:56818600-56832000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:56818800-56820200	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr3:56818800-56820200	Genic enhancers	Thymus	Thymus
38	chr3:56818800-56821200	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr3:56818800-56821400	Weak transcription	Small Intestine	intestine
40	chr3:56818800-56822200	Weak transcription	Colonic Mucosa	Colon
41	chr3:56818800-56822200	Weak transcription	Colon Smooth Muscle	Colon
42	chr3:56818800-56822200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr3:56818800-56822600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr3:56819000-56821200	Weak transcription	Fetal Lung	lung
45	chr3:56819000-56829000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr3:56819000-56830400	Weak transcription	HSMM	muscle
47	chr3:56819200-56820400	Weak transcription	Brain Anterior Caudate	brain
48	chr3:56819200-56821200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:56819200-56821200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:56819200-56821400	Enhancers	GM12878-XiMat	blood

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