Variant report

Variant	rs13319627
Chromosome Location	chr3:56769446-56769447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1009118	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1009119	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11919114	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11919130	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11919184	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12233433	0.86[AMR][1000 genomes]
rs13061142	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13095559	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1489948	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1844474	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1844475	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28651361	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34360725	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34924415	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3732511	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821414	0.91[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3901349	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3924228	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs41276471	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4521191	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4574264	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs55651418	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55849986	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56031438	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56097266	0.86[AMR][1000 genomes]
rs56152533	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6445822	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6445823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6765444	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6767897	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6770654	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6773569	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6776368	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6776992	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6777946	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6778753	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6778984	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6778985	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6780940	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6781979	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6781995	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6783263	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6787106	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6792623	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6793398	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6794215	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6804621	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6805864	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6808707	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6978	1.00[ASW][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7427683	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7427684	0.90[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7431479	1.00[CEU][hapmap];0.88[JPT][hapmap];0.98[EUR][1000 genomes]
rs7617179	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7627227	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7650042	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9311618	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311619	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957849	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9754631	0.92[ASN][1000 genomes]
rs9755927	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9757026	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9810507	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9810658	0.84[AMR][1000 genomes]
rs9816311	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9826255	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9826362	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9826563	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9835767	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9845925	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9855217	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9864273	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9864804	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9865146	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9866237	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9882705	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9883232	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[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	esv3440152	chr3:56764403-56773941	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13319627	ARHGEF3	cis	lymphoblastoid	seeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56754400-56783200	Weak transcription	Stomach Mucosa	stomach
2	chr3:56755200-56781800	Weak transcription	NH-A	brain
3	chr3:56756800-56781000	Weak transcription	Fetal Intestine Large	intestine
4	chr3:56757000-56786400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:56757600-56792200	Weak transcription	Hela-S3	cervix
6	chr3:56758600-56792200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:56758800-56770800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:56758800-56782800	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr3:56759000-56774400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:56759400-56784000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:56759600-56773200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:56759800-56779000	Weak transcription	Liver	Liver
13	chr3:56759800-56790400	Strong transcription	Dnd41	blood
14	chr3:56760400-56773200	Strong transcription	Primary B cells from cord blood	blood
15	chr3:56760800-56773200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr3:56760800-56783000	Weak transcription	Osteobl	bone
17	chr3:56760800-56788800	Strong transcription	Fetal Thymus	thymus
18	chr3:56762000-56788400	Weak transcription	Colonic Mucosa	Colon
19	chr3:56763600-56781000	Weak transcription	Fetal Brain Male	brain
20	chr3:56763600-56784200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:56763800-56771000	Weak transcription	Fetal Lung	lung
22	chr3:56763800-56789000	Weak transcription	Small Intestine	intestine
23	chr3:56763800-56790200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:56763800-56792800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:56764000-56770200	Weak transcription	Brain Germinal Matrix	brain
26	chr3:56764000-56770800	Weak transcription	Ovary	ovary
27	chr3:56764000-56770800	Weak transcription	Right Ventricle	heart
28	chr3:56764000-56771000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:56764000-56783200	Weak transcription	HSMMtube	muscle
30	chr3:56764000-56783400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:56764000-56786600	Weak transcription	Aorta	Aorta
32	chr3:56764000-56788800	Weak transcription	Fetal Heart	heart
33	chr3:56764000-56789000	Weak transcription	Psoas Muscle	Psoas
34	chr3:56764000-56793400	Weak transcription	Gastric	stomach
35	chr3:56764000-56815800	Weak transcription	Fetal Intestine Small	intestine
36	chr3:56764200-56777200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:56764600-56770000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:56765200-56778200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:56766200-56771400	Genic enhancers	Primary T cells fromperipheralblood	blood
40	chr3:56766200-56788200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr3:56766400-56770200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:56766400-56770400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:56766400-56770800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:56766400-56771000	Weak transcription	Brain Anterior Caudate	brain
45	chr3:56766400-56776400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:56766400-56777400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr3:56766400-56777600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr3:56766400-56777800	Weak transcription	Fetal Brain Female	brain
49	chr3:56766600-56769600	Weak transcription	Adipose Nuclei	Adipose
50	chr3:56766600-56770800	Weak transcription	Pancreas	Pancrea

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