Variant report

Variant	rs58189274
Chromosome Location	chr3:51586935-51586936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10510758	0.82[ASN][1000 genomes]
rs12485610	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12486568	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12487426	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12489414	0.83[ASN][1000 genomes]
rs12490471	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12491048	0.81[ASN][1000 genomes]
rs12492624	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12493265	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12493618	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12493857	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12494462	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12494979	0.82[ASN][1000 genomes]
rs12496340	0.93[EUR][1000 genomes]
rs13089799	0.87[EUR][1000 genomes]
rs13090348	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13324384	0.87[EUR][1000 genomes]
rs17051783	0.82[ASN][1000 genomes]
rs17051811	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17661242	0.82[ASN][1000 genomes]
rs17712228	0.83[ASN][1000 genomes]
rs2033703	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2082992	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2082993	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2217938	0.82[ASN][1000 genomes]
rs2241785	0.81[ASN][1000 genomes]
rs2304512	0.82[ASN][1000 genomes]
rs2356261	0.82[ASN][1000 genomes]
rs2356298	0.88[ASN][1000 genomes]
rs35536327	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3749317	0.82[ASN][1000 genomes]
rs3792408	0.82[ASN][1000 genomes]
rs3804766	0.82[ASN][1000 genomes]
rs4687553	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687563	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4687592	0.81[EUR][1000 genomes]
rs4687599	0.87[EUR][1000 genomes]
rs4687601	0.82[ASN][1000 genomes]
rs4687605	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4687610	0.83[ASN][1000 genomes]
rs4687656	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687691	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4687731	0.82[ASN][1000 genomes]
rs4687769	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4687777	0.82[ASN][1000 genomes]
rs4687794	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4687811	0.83[ASN][1000 genomes]
rs4687812	0.82[ASN][1000 genomes]
rs4687813	0.82[ASN][1000 genomes]
rs55667499	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55706150	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55872019	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56239081	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56729479	0.88[ASN][1000 genomes]
rs57027950	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57831708	0.81[ASN][1000 genomes]
rs58059174	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58568178	0.82[ASN][1000 genomes]
rs58762652	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58836277	0.82[ASN][1000 genomes]
rs59564034	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59838596	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60007226	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60606339	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61233013	0.91[ASN][1000 genomes]
rs61419317	0.82[ASN][1000 genomes]
rs61689323	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72951443	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72951490	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7375146	0.87[EUR][1000 genomes]
rs73834252	0.82[ASN][1000 genomes]
rs73834253	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73834254	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73834258	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73834265	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73837442	0.82[ASN][1000 genomes]
rs73837443	0.82[ASN][1000 genomes]
rs7642698	0.83[ASN][1000 genomes]
rs9820140	0.81[ASN][1000 genomes]
rs9827186	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9842600	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9843583	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9861019	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv997264	chr3:51584056-51689648	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv536570	chr3:51584056-51689648	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv999553	chr3:51584056-51696052	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51573800-51594000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:51574000-51590800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:51574000-51593800	Weak transcription	Right Ventricle	heart
4	chr3:51574000-51597000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:51574000-51600600	Weak transcription	Gastric	stomach
6	chr3:51574000-51615400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:51574000-51624800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:51574200-51616400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:51574400-51593200	Weak transcription	Brain Angular Gyrus	brain
10	chr3:51574400-51613800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:51574600-51587400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:51574600-51590800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr3:51574600-51593200	Weak transcription	Brain Anterior Caudate	brain
14	chr3:51574600-51593200	Weak transcription	NHLF	lung
15	chr3:51574600-51593400	Weak transcription	HSMMtube	muscle
16	chr3:51574600-51593800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:51574600-51593800	Weak transcription	Left Ventricle	heart
18	chr3:51574600-51594400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:51574600-51600800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:51574600-51601800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:51574600-51624600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:51574800-51591000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:51574800-51597600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:51574800-51624800	Weak transcription	NH-A	brain
25	chr3:51575000-51587400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:51575000-51597400	Weak transcription	Small Intestine	intestine
27	chr3:51575200-51587600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:51575200-51615600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:51575600-51587400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:51575600-51593200	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:51576000-51595400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:51576200-51593000	Strong transcription	Fetal Stomach	stomach
33	chr3:51576400-51593200	Weak transcription	HSMM	muscle
34	chr3:51576400-51597800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:51576400-51602000	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:51577200-51597600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:51578600-51587600	Weak transcription	Fetal Intestine Large	intestine
38	chr3:51578600-51587600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr3:51578600-51591400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:51578600-51607000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:51578800-51587600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:51578800-51593400	Weak transcription	NHDF-Ad	bronchial
43	chr3:51578800-51597400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr3:51578800-51600200	Weak transcription	A549	lung
45	chr3:51578800-51624400	Weak transcription	Esophagus	oesophagus
46	chr3:51579000-51593600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:51579000-51602000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:51579200-51602400	Weak transcription	HMEC	breast
49	chr3:51579600-51589800	Strong transcription	Fetal Intestine Small	intestine
50	chr3:51580000-51602600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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