Variant report

Variant	rs11130547
Chromosome Location	chr3:56808770-56808771
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10510788	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1110866	0.81[AMR][1000 genomes]
rs12054242	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17235733	0.81[AMR][1000 genomes]
rs17288908	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2317250	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2317251	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35550387	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55837354	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55993130	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56122263	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56134339	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56201611	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57620263	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58478669	0.87[AMR][1000 genomes]
rs60374893	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60882397	0.85[AMR][1000 genomes]
rs62252679	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6795927	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7611544	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7625636	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7629147	0.84[AMR][1000 genomes]
rs984796	0.95[AMR][1000 genomes];0.89[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
rs11130547	ARHGEF3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56764000-56815800	Weak transcription	Fetal Intestine Small	intestine
2	chr3:56792600-56809600	Weak transcription	Small Intestine	intestine
3	chr3:56793200-56817400	Weak transcription	Hela-S3	cervix
4	chr3:56793600-56809600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:56796600-56809800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:56796800-56809600	Weak transcription	NHLF	lung
7	chr3:56796800-56816400	Weak transcription	Colonic Mucosa	Colon
8	chr3:56797200-56809200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:56797600-56811400	Weak transcription	Stomach Mucosa	stomach
10	chr3:56799000-56815800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:56800800-56809000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:56802600-56811800	Strong transcription	Dnd41	blood
13	chr3:56803200-56809200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:56803200-56809600	Strong transcription	Thymus	Thymus
15	chr3:56803400-56810400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:56803600-56809600	Weak transcription	Fetal Kidney	kidney
17	chr3:56804000-56809000	Weak transcription	Brain Substantia Nigra	brain
18	chr3:56804200-56809000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:56804200-56809600	Weak transcription	Brain Angular Gyrus	brain
20	chr3:56804200-56809600	Weak transcription	Right Atrium	heart
21	chr3:56804200-56810000	Strong transcription	Fetal Thymus	thymus
22	chr3:56804200-56810000	Weak transcription	Psoas Muscle	Psoas
23	chr3:56804600-56810200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:56805600-56809800	Strong transcription	HepG2	liver
25	chr3:56805800-56809400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr3:56805800-56809400	Weak transcription	Brain Germinal Matrix	brain
27	chr3:56805800-56809800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:56805800-56816800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:56806000-56809000	Strong transcription	Primary T cells from cord blood	blood
30	chr3:56806000-56809400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:56806400-56809400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:56806400-56809600	Weak transcription	Gastric	stomach
33	chr3:56806400-56809600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:56806400-56809600	Weak transcription	Spleen	Spleen
35	chr3:56806400-56815800	Weak transcription	Esophagus	oesophagus
36	chr3:56806400-56816800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:56806400-56817000	Weak transcription	NHEK	skin
38	chr3:56806600-56809000	Weak transcription	Brain Anterior Caudate	brain
39	chr3:56806600-56809600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr3:56807000-56833200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr3:56807200-56809400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr3:56807400-56811000	Enhancers	Fetal Brain Male	brain
43	chr3:56807400-56814000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:56807400-56814600	Genic enhancers	Primary T cells fromperipheralblood	blood
45	chr3:56807400-56816000	Weak transcription	Fetal Intestine Large	intestine
46	chr3:56807600-56808800	Enhancers	Left Ventricle	heart
47	chr3:56807600-56808800	Enhancers	Ovary	ovary
48	chr3:56807600-56810200	Weak transcription	Adipose Nuclei	Adipose
49	chr3:56807600-56811000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr3:56807600-56818000	Weak transcription	Fetal Muscle Trunk	muscle

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