Variant report

Variant	rs58249114
Chromosome Location	chr3:53056991-53056992
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53056801..53057547-chr3:53179048..53179588,2	MCF-7	breast:
2	chr3:53047316..53051698-chr3:53056732..53062167,5	MCF-7	breast:
3	chr3:53056126..53058134-chr3:53061359..53063994,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs56665986	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56835905	0.92[AFR][1000 genomes]
rs56895623	1.00[AFR][1000 genomes]
rs57273027	0.84[AFR][1000 genomes]
rs57465047	0.92[AFR][1000 genomes]
rs57561909	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57654423	0.86[AFR][1000 genomes]
rs58888768	0.92[AFR][1000 genomes]
rs59224641	0.98[AFR][1000 genomes]
rs59838592	0.95[AFR][1000 genomes]
rs60648378	0.98[AFR][1000 genomes]
rs61324750	0.86[AFR][1000 genomes]
rs61331336	0.85[AFR][1000 genomes]
rs61437303	0.92[AFR][1000 genomes]
rs61438885	0.92[AFR][1000 genomes]
rs6798309	0.98[AFR][1000 genomes]
rs6798669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72959475	0.84[AFR][1000 genomes]
rs72959477	0.84[AFR][1000 genomes]
rs72959478	0.87[AFR][1000 genomes]
rs72959479	0.84[AFR][1000 genomes]
rs72959482	0.84[AFR][1000 genomes]
rs72959487	0.84[AFR][1000 genomes]
rs72959494	0.86[AFR][1000 genomes]
rs72959499	0.87[AFR][1000 genomes]
rs72961704	0.84[AFR][1000 genomes]
rs72961705	0.86[AFR][1000 genomes]
rs72961708	0.86[AFR][1000 genomes]
rs72961724	0.92[AFR][1000 genomes]
rs72961730	0.92[AFR][1000 genomes]
rs72961733	0.92[AFR][1000 genomes]
rs72961742	0.98[AFR][1000 genomes]
rs72961752	0.98[AFR][1000 genomes]
rs72965340	1.00[AFR][1000 genomes]
rs72965348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965358	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965366	0.92[AFR][1000 genomes]
rs72965370	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965381	0.93[AFR][1000 genomes]
rs7618417	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv876799	chr3:53024216-53060637	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv590321	chr3:53027983-53062661	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv876800	chr3:53038786-53113762	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv1823728	chr3:53046712-53080351	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv1820544	chr3:53046712-53096394	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers 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:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53019000-53057200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr3:53020600-53057000	Weak transcription	Dnd41	blood
3	chr3:53025600-53061600	Weak transcription	Lung	lung
4	chr3:53027600-53061600	Weak transcription	Liver	Liver
5	chr3:53030200-53059400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:53033000-53078400	Weak transcription	Aorta	Aorta
7	chr3:53033200-53057000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:53033800-53060400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:53033800-53065000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:53037000-53065000	Weak transcription	Fetal Intestine Small	intestine
11	chr3:53040800-53065000	Weak transcription	Fetal Intestine Large	intestine
12	chr3:53043800-53064800	Weak transcription	Stomach Mucosa	stomach
13	chr3:53044600-53065000	Weak transcription	Gastric	stomach
14	chr3:53045200-53061400	Weak transcription	Fetal Heart	heart
15	chr3:53045400-53057200	Weak transcription	Psoas Muscle	Psoas
16	chr3:53045400-53061600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:53045600-53057000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:53045600-53057600	Weak transcription	Left Ventricle	heart
19	chr3:53045800-53061400	Weak transcription	HepG2	liver
20	chr3:53046000-53057600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:53048400-53058600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:53048800-53077800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:53049200-53059800	Weak transcription	Pancreas	Pancrea
24	chr3:53050600-53057200	Weak transcription	Small Intestine	intestine
25	chr3:53050600-53062000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:53052000-53064800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:53052800-53057000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr3:53053000-53057200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:53053000-53057400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:53053000-53057600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:53053000-53063600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:53053200-53057000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:53053200-53057600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:53053400-53058200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:53053800-53061600	Weak transcription	Ovary	ovary
36	chr3:53054000-53070600	Weak transcription	Right Ventricle	heart
37	chr3:53054400-53059800	Weak transcription	Primary B cells from cord blood	blood
38	chr3:53054400-53064800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr3:53055600-53057200	Weak transcription	Brain Germinal Matrix	brain
40	chr3:53055600-53058400	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr3:53055600-53060800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:53056000-53058000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:53056200-53059600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr3:53056400-53057800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr3:53056400-53058000	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr3:53056600-53057800	Enhancers	Primary T cells from cord blood	blood
47	chr3:53056600-53057800	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr3:53056600-53057800	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr3:53056600-53058200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:53056600-53058800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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