Variant report

Variant	rs574942
Chromosome Location	chr3:138399934-138399935
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138397969..138401345-chr3:138402336..138404310,3	K562	blood:
2	chr3:138399261..138401843-chr3:138404364..138407341,4	K562	blood:
3	chr3:138398972..138402423-chr3:138404344..138407702,4	K562	blood:

Variant related genes	Relation type
ENSG00000051382	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1066197	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1068104	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1068685	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11705762	1.00[ASN][1000 genomes]
rs11709768	1.00[ASN][1000 genomes]
rs11713049	1.00[ASN][1000 genomes]
rs11720178	1.00[ASN][1000 genomes]
rs11924814	1.00[ASN][1000 genomes]
rs13069296	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13082808	1.00[ASN][1000 genomes]
rs13433948	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1400266	1.00[ASN][1000 genomes]
rs1663554	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1663556	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673597	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs187245	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191713	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191714	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191775	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2197387	1.00[ASN][1000 genomes]
rs244380	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs244381	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2595928	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2595930	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2595932	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607108	0.89[ASN][1000 genomes]
rs2607109	0.89[ASN][1000 genomes]
rs2607796	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28376988	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28408150	1.00[ASN][1000 genomes]
rs34900559	0.89[ASN][1000 genomes]
rs35214574	1.00[ASN][1000 genomes]
rs361054	1.00[ASN][1000 genomes]
rs361055	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361056	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361057	0.86[EUR][1000 genomes]
rs361059	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361060	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361061	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs361062	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361063	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361064	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361065	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361066	1.00[ASN][1000 genomes]
rs361067	1.00[ASN][1000 genomes]
rs361068	1.00[ASN][1000 genomes]
rs361071	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361072	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs361079	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361080	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361081	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361082	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361083	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361084	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361085	0.89[ASN][1000 genomes]
rs361088	0.86[EUR][1000 genomes]
rs361089	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs361092	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs361094	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361096	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361097	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs371762	1.00[ASN][1000 genomes]
rs385254	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398065	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404110	1.00[ASN][1000 genomes]
rs409507	1.00[ASN][1000 genomes]
rs413147	1.00[ASN][1000 genomes]
rs4305444	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439720	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs470359	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs473388	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs475254	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs476800	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs482334	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894350	1.00[ASN][1000 genomes]
rs4894351	1.00[ASN][1000 genomes]
rs4894352	1.00[ASN][1000 genomes]
rs4894353	1.00[ASN][1000 genomes]
rs4894354	1.00[ASN][1000 genomes]
rs491371	0.82[ASN][1000 genomes]
rs493152	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs497900	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500687	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524164	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531577	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs539619	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540198	1.00[ASN][1000 genomes]
rs550768	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs558905	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559160	0.87[EUR][1000 genomes]
rs559451	0.82[AMR][1000 genomes]
rs564455	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs589986	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603723	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs607044	1.00[ASN][1000 genomes]
rs618457	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs621204	0.86[EUR][1000 genomes]
rs62282169	1.00[ASN][1000 genomes]
rs624099	0.87[EUR][1000 genomes]
rs625468	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs635592	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6439817	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs647972	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs654459	0.84[AFR][1000 genomes]
rs6776585	1.00[ASN][1000 genomes]
rs6795203	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6801207	1.00[ASN][1000 genomes]
rs7612106	1.00[ASN][1000 genomes]
rs7615854	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7643722	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773045	0.87[EUR][1000 genomes]
rs773184	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9821694	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822714	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832012	1.00[ASN][1000 genomes]
rs9834963	1.00[ASN][1000 genomes]
rs9864176	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874723	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879784	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138360800-138407600	Weak transcription	HUVEC	blood vessel
2	chr3:138364400-138459200	Weak transcription	Psoas Muscle	Psoas
3	chr3:138368800-138400200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:138368800-138422600	Weak transcription	Right Atrium	heart
5	chr3:138369000-138493000	Weak transcription	Fetal Lung	lung
6	chr3:138369200-138401600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:138369200-138412800	Weak transcription	Hela-S3	cervix
8	chr3:138369200-138428800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:138369200-138435600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:138375200-138429000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:138383000-138404800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:138383200-138412800	Weak transcription	Ovary	ovary
13	chr3:138383200-138448200	Weak transcription	Gastric	stomach
14	chr3:138383400-138426400	Weak transcription	Spleen	Spleen
15	chr3:138383400-138443000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:138383800-138400200	Weak transcription	Fetal Kidney	kidney
17	chr3:138383800-138405400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:138385000-138418400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:138389200-138401200	Weak transcription	Brain Substantia Nigra	brain
20	chr3:138389200-138405000	Weak transcription	Small Intestine	intestine
21	chr3:138390800-138459600	Weak transcription	Right Ventricle	heart
22	chr3:138391200-138422000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:138392200-138405600	Weak transcription	Stomach Mucosa	stomach
24	chr3:138393200-138401000	Weak transcription	Brain Angular Gyrus	brain
25	chr3:138393200-138405600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:138393200-138407800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr3:138393600-138400200	Weak transcription	HepG2	liver
28	chr3:138393600-138405600	Weak transcription	HSMM	muscle
29	chr3:138393800-138515000	Weak transcription	Aorta	Aorta
30	chr3:138394000-138401000	Weak transcription	Left Ventricle	heart
31	chr3:138394000-138404800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:138394000-138418600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:138394400-138413000	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:138395200-138436800	Weak transcription	Brain Germinal Matrix	brain
35	chr3:138395400-138400200	Weak transcription	Fetal Heart	heart
36	chr3:138395400-138402200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:138395800-138400200	Weak transcription	Brain Anterior Caudate	brain
38	chr3:138395800-138400200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:138395800-138400200	Weak transcription	A549	lung
40	chr3:138395800-138400400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr3:138395800-138400400	Weak transcription	Osteobl	bone
42	chr3:138395800-138401200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr3:138395800-138402800	Weak transcription	GM12878-XiMat	blood
44	chr3:138395800-138405400	Weak transcription	NH-A	brain
45	chr3:138395800-138405600	Weak transcription	NHDF-Ad	bronchial
46	chr3:138395800-138413400	Weak transcription	HSMMtube	muscle
47	chr3:138395800-138444800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:138395800-138459800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:138395800-138480200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr3:138396000-138400600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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