Variant report

Variant	rs4490402
Chromosome Location	chr3:46107037-46107038
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46096990..46098944-chr3:46105207..46107426,2	K562	blood:
2	chr3:46036104..46038471-chr3:46105793..46108265,2	MCF-7	breast:
3	chr3:46106956..46110561-chr3:46110945..46113902,3	K562	blood:

Variant related genes	Relation type
ENSG00000163820	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10510747	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1118021	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12054287	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs12486449	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13320534	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs13434141	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1392290	0.82[JPT][hapmap]
rs1491960	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1546079	0.87[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs1602580	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1604068	0.98[ASN][1000 genomes]
rs17078567	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17078589	0.91[ASN][1000 genomes]
rs2036295	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2173639	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2888512	0.89[ASN][1000 genomes]
rs3796376	0.89[CEU][hapmap]
rs3851347	0.82[JPT][hapmap]
rs4339141	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4447807	0.86[EUR][1000 genomes]
rs4586860	0.89[ASN][1000 genomes]
rs4682804	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4682805	0.90[ASN][1000 genomes]
rs4682807	0.90[ASN][1000 genomes]
rs4683169	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4683174	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56800498	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58035200	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58260031	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59865404	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60539039	0.88[EUR][1000 genomes]
rs60991632	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61066315	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61254379	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61387489	0.89[ASN][1000 genomes]
rs62242832	0.86[EUR][1000 genomes]
rs62242846	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62243869	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62243873	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62243875	0.87[EUR][1000 genomes]
rs62243876	0.87[EUR][1000 genomes]
rs62243906	0.83[EUR][1000 genomes]
rs6764042	0.82[JPT][hapmap]
rs6778958	0.89[ASN][1000 genomes]
rs6780163	0.82[JPT][hapmap]
rs6807854	0.86[EUR][1000 genomes]
rs751625	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7623460	0.82[JPT][hapmap]
rs7623476	0.95[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7641151	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7641164	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7643426	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs880160	0.89[ASN][1000 genomes]
rs9818635	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9849715	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9856805	0.90[ASN][1000 genomes]
rs9990060	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv1805205	chr3:46032847-46111081	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46103400-46113600	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr3:46103800-46113200	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr3:46103800-46114200	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr3:46104000-46113400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr3:46104200-46108400	Enhancers	Fetal Thymus	thymus
6	chr3:46104200-46110000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:46104200-46110200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr3:46104200-46113600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:46104400-46111800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:46104600-46114000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:46104800-46109200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:46105000-46108600	Weak transcription	Spleen	Spleen
13	chr3:46105000-46109800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:46105200-46108600	Weak transcription	Aorta	Aorta
15	chr3:46105200-46111000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr3:46105400-46111000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr3:46105600-46107200	Weak transcription	Adipose Nuclei	Adipose
18	chr3:46105600-46107600	Enhancers	Fetal Heart	heart
19	chr3:46105800-46107200	Enhancers	Dnd41	blood
20	chr3:46105800-46107600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr3:46106000-46107600	Enhancers	Right Atrium	heart
22	chr3:46106200-46107600	Bivalent Enhancer	Thymus	Thymus
23	chr3:46106400-46111200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr3:46106600-46107200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:46106600-46107400	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr3:46106600-46107600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:46106600-46108200	Bivalent Enhancer	Fetal Muscle Leg	muscle
28	chr3:46106800-46107200	Enhancers	Lung	lung
29	chr3:46106800-46107400	Bivalent Enhancer	HSMMtube	muscle
30	chr3:46106800-46107600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:46106800-46107600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:46106800-46107800	Enhancers	Right Ventricle	heart
33	chr3:46107000-46107200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:46107000-46107200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr3:46107000-46107200	Enhancers	GM12878-XiMat	blood
36	chr3:46107000-46107400	Enhancers	Placenta Amnion	Placenta Amnion
37	chr3:46107000-46107400	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr3:46107000-46107400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr3:46107000-46107400	Enhancers	HMEC	breast
40	chr3:46107000-46107600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:46107000-46107600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
42	chr3:46107000-46107600	Enhancers	Placenta	Placenta
43	chr3:46107000-46107600	Enhancers	Left Ventricle	heart
44	chr3:46107000-46107600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr3:46107000-46109800	Enhancers	Psoas Muscle	Psoas

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