Variant report

Variant	rs288239
Chromosome Location	chr2:183645816-183645817
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1037404	0.81[EUR][1000 genomes]
rs11901549	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13509	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1452312	0.85[AFR][1000 genomes]
rs167013	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs184078	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs190830	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs192618	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs208393	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs288240	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs288241	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs288253	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288254	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288256	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288257	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288258	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288259	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288260	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs288263	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs288264	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs288265	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs288267	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs288268	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs288269	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs288271	0.81[ASN][1000 genomes]
rs288278	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288280	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288283	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs288285	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288287	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288289	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs288291	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288292	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288293	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288294	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288295	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288296	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288299	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs288300	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs288302	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs288303	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs288304	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs288305	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs288306	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs288307	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs288308	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs288309	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs288310	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs288311	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs288312	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs288313	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs288331	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288332	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288334	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288335	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs288336	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs288342	0.82[AFR][1000 genomes]
rs288347	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs288349	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3115425	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34818934	0.85[EUR][1000 genomes]
rs369573	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs384190	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs409343	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs418159	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs418474	0.86[ASN][1000 genomes]
rs432527	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs438248	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs442044	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62188170	0.83[EUR][1000 genomes]
rs6727545	0.85[EUR][1000 genomes]
rs6745697	0.83[EUR][1000 genomes]
rs73975514	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7588247	0.85[EUR][1000 genomes]
rs825660	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs825668	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9677291	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9678817	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2757842	chr2:183437700-183835084	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759104	chr2:183437700-183835084	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2756954	chr2:183528670-183764930	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv875483	chr2:183537399-183657867	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	esv34847	chr2:183537399-183786763	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	esv3693445	chr2:183542825-183725221	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs288239	FRZB	cis	Artery Tibial	GTEx
rs288239	DNAJC10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183581800-183647600	Weak transcription	Gastric	stomach
2	chr2:183581800-183655600	Weak transcription	Pancreas	Pancrea
3	chr2:183605600-183646000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:183609000-183646600	Weak transcription	Hela-S3	cervix
5	chr2:183623200-183651400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:183625000-183647000	Weak transcription	Placenta	Placenta
7	chr2:183625000-183648000	Weak transcription	Right Ventricle	heart
8	chr2:183625000-183650600	Weak transcription	Stomach Mucosa	stomach
9	chr2:183626000-183647200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:183627200-183647200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:183627200-183652600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:183627200-183657800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:183627400-183647000	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:183627400-183652400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr2:183628400-183647000	Weak transcription	Brain Angular Gyrus	brain
16	chr2:183629200-183647800	Weak transcription	K562	blood
17	chr2:183629800-183647200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:183630200-183647200	Weak transcription	NHDF-Ad	bronchial
19	chr2:183630400-183646800	Weak transcription	Fetal Brain Male	brain
20	chr2:183631000-183652800	Weak transcription	NHLF	lung
21	chr2:183631600-183653400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:183632400-183648200	Weak transcription	Fetal Heart	heart
23	chr2:183632800-183647200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr2:183633400-183647200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:183633600-183647000	Weak transcription	HSMMtube	muscle
26	chr2:183633600-183647200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:183633800-183652800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:183633800-183657800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:183634200-183647200	Weak transcription	Brain Substantia Nigra	brain
30	chr2:183638000-183652400	Weak transcription	Brain Anterior Caudate	brain
31	chr2:183638600-183646000	Strong transcription	Primary B cells from peripheral blood	blood
32	chr2:183638800-183646000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:183638800-183646200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:183639000-183646000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr2:183639000-183646200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:183639000-183646200	Strong transcription	Primary B cells from cord blood	blood
37	chr2:183639400-183647200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr2:183639600-183646400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:183639600-183646800	Weak transcription	Fetal Stomach	stomach
40	chr2:183639600-183646800	Weak transcription	Spleen	Spleen
41	chr2:183639600-183647400	Weak transcription	Ovary	ovary
42	chr2:183639800-183653400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:183639800-183654600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:183640200-183646000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:183640400-183646000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:183640600-183646800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr2:183641200-183652400	Weak transcription	Brain Germinal Matrix	brain
48	chr2:183641400-183647600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr2:183641400-183649800	Weak transcription	Fetal Brain Female	brain
50	chr2:183642000-183646000	Strong transcription	Primary T cells from cord blood	blood

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