Variant report

Variant	rs2317251
Chromosome Location	chr3:56812738-56812739
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10510788	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11130547	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12054242	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17288908	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2317250	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35550387	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55837354	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55993130	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56122263	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56134339	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56201611	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57620263	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58478669	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs60374893	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60882397	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62252679	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6795927	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7611544	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7625636	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs984796	0.91[AMR][1000 genomes];0.90[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
rs2317251	ARHGEF3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56764000-56815800	Weak transcription	Fetal Intestine Small	intestine
2	chr3:56793200-56817400	Weak transcription	Hela-S3	cervix
3	chr3:56796800-56816400	Weak transcription	Colonic Mucosa	Colon
4	chr3:56799000-56815800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:56805800-56816800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:56806400-56815800	Weak transcription	Esophagus	oesophagus
7	chr3:56806400-56816800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:56806400-56817000	Weak transcription	NHEK	skin
9	chr3:56807000-56833200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:56807400-56814000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:56807400-56814600	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr3:56807400-56816000	Weak transcription	Fetal Intestine Large	intestine
13	chr3:56807600-56818000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr3:56807800-56817400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:56808000-56813000	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr3:56808000-56815800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:56808000-56815800	Weak transcription	HUVEC	blood vessel
18	chr3:56808200-56816800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:56808600-56816800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr3:56809000-56816800	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr3:56809400-56815800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr3:56809600-56813800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:56809800-56812800	Weak transcription	HepG2	liver
24	chr3:56810000-56815800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:56810000-56816600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:56810000-56822200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:56810200-56813000	Weak transcription	Primary B cells from cord blood	blood
28	chr3:56810200-56817000	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr3:56810400-56815000	Weak transcription	Thymus	Thymus
30	chr3:56810400-56815400	Weak transcription	Psoas Muscle	Psoas
31	chr3:56810400-56816000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:56810400-56816400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:56810400-56816400	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:56810400-56817000	Weak transcription	Right Ventricle	heart
35	chr3:56810400-56817000	Weak transcription	Spleen	Spleen
36	chr3:56810400-56818000	Weak transcription	Placenta	Placenta
37	chr3:56810400-56819000	Weak transcription	Fetal Brain Female	brain
38	chr3:56810600-56815800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:56810600-56815800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:56810800-56816200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:56810800-56816400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr3:56811000-56814200	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:56811000-56815600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:56811000-56815800	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:56811000-56815800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:56811000-56815800	Weak transcription	HMEC	breast
47	chr3:56811000-56816400	Weak transcription	Brain Anterior Caudate	brain
48	chr3:56811000-56816400	Weak transcription	Fetal Lung	lung
49	chr3:56811200-56814000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr3:56811200-56815800	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links