Variant report

Variant	rs520904
Chromosome Location	chr3:138369281-138369282
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138366382..138369561-chr3:138372165..138374975,3	K562	blood:
2	chr3:138327553..138329730-chr3:138368846..138371731,2	K562	blood:
3	chr3:138369214..138371379-chr3:138655274..138656934,2	K562	blood:

Variant related genes	Relation type
ENSG00000158234	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1068685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10804658	1.00[CHB][hapmap]
rs1091528	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11720178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs1663554	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1673597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs191714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap]
rs191775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2607796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2881900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs361057	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs361059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs361060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs361062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs361063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361066	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs361067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs361072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs361073	1.00[CHB][hapmap]
rs361074	1.00[CHB][hapmap]
rs361075	1.00[CHB][hapmap]
rs361076	1.00[CHB][hapmap]
rs361077	1.00[CHB][hapmap]
rs361080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs361082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361087	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361088	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs361096	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs385254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs413147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs4305444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs484698	1.00[CHB][hapmap]
rs4894359	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs493152	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs497900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs500687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap]
rs523975	1.00[CHB][hapmap]
rs524164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs531577	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs537894	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs542010	0.82[MEX][hapmap]
rs558905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs559160	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs564455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs600590	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs601032	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs603723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs624099	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap]
rs635592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs643620	1.00[CHB][hapmap]
rs6439817	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6773514	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs6784610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap]
rs7613579	0.96[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs7643722	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap]
rs773045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs774015	1.00[CHB][hapmap]
rs811322	1.00[CHB][hapmap]
rs9289566	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs9647336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9647337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap]
rs9821694	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9822714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9834963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9879784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv967070	chr3:138355155-138372373	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
10	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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138340400-138393800	Weak transcription	Fetal Brain Male	brain
2	chr3:138360600-138372000	Weak transcription	NH-A	brain
3	chr3:138360800-138407600	Weak transcription	HUVEC	blood vessel
4	chr3:138364400-138459200	Weak transcription	Psoas Muscle	Psoas
5	chr3:138367200-138374200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:138367400-138370200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
7	chr3:138367600-138369400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:138367600-138369400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
9	chr3:138367600-138369400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:138367600-138369400	Strong transcription	Brain Anterior Caudate	brain
11	chr3:138367600-138369800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
12	chr3:138367600-138369800	Strong transcription	Primary T cells from cord blood	blood
13	chr3:138367600-138370200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
14	chr3:138367600-138370800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
15	chr3:138367600-138381000	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr3:138367800-138369400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:138367800-138369400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
18	chr3:138367800-138369400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr3:138367800-138369400	Strong transcription	Brain Hippocampus Middle	brain
20	chr3:138367800-138369400	Strong transcription	Brain Inferior Temporal Lobe	brain
21	chr3:138367800-138369400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
22	chr3:138367800-138369600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
23	chr3:138367800-138369600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:138367800-138369800	Strong transcription	Brain Cingulate Gyrus	brain
25	chr3:138367800-138369800	Strong transcription	Osteobl	bone
26	chr3:138367800-138377600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:138368000-138369400	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
28	chr3:138368000-138369400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:138368000-138369400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:138368000-138369800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:138368000-138370400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr3:138368000-138370800	Strong transcription	Stomach Smooth Muscle	stomach
33	chr3:138368000-138372600	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:138368000-138374000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:138368000-138376800	Strong transcription	Left Ventricle	heart
36	chr3:138368000-138377800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:138368000-138378200	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr3:138368200-138369400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:138368200-138369400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr3:138368200-138369400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr3:138368200-138369400	Strong transcription	Rectal Smooth Muscle	rectum
42	chr3:138368200-138369600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr3:138368200-138370000	Strong transcription	Small Intestine	intestine
44	chr3:138368400-138369400	Strong transcription	NHEK	skin
45	chr3:138368400-138369600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:138368400-138369600	Strong transcription	Gastric	stomach
47	chr3:138368400-138370000	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr3:138368400-138372600	Weak transcription	HepG2	liver
49	chr3:138368400-138372800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:138368400-138380200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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