Variant report

Variant	rs60415551
Chromosome Location	chr3:52572648-52572649
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52569931..52572827-chr3:52736282..52738188,2	K562	blood:
2	chr3:52570878..52573539-chr3:52577904..52579826,2	K562	blood:
3	chr3:52536407..52539525-chr3:52571038..52574825,3	K562	blood:
4	chr3:52488315..52491899-chr3:52569459..52572680,4	MCF-7	breast:
5	chr3:52008086..52010080-chr3:52571310..52572839,2	K562	blood:
6	chr3:52539372..52542636-chr3:52569567..52572921,4	MCF-7	breast:
7	chr3:52571791..52573974-chr3:52596279..52597923,2	K562	blood:

Variant related genes	Relation type
ENSG00000016864	Chromatin interaction
ENSG00000010327	Chromatin interaction
ENSG00000114786	Chromatin interaction
ENSG00000248487	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000010322	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10510759	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12107484	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1987234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34173244	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35920544	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56156188	0.84[AFR][1000 genomes]
rs56259931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56960576	1.00[EUR][1000 genomes]
rs57008939	0.84[AFR][1000 genomes]
rs57246324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57298447	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57319306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57560655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57757646	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs57869735	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58100002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58725214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58924550	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60311166	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60611300	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60682984	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60823713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60916588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61220667	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61538294	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6445536	0.85[AMR][1000 genomes]
rs6780005	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72947535	0.96[AFR][1000 genomes]
rs72947580	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72947583	1.00[EUR][1000 genomes]
rs72947584	1.00[EUR][1000 genomes]
rs72947589	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950430	0.85[AFR][1000 genomes]
rs72950432	0.83[AFR][1000 genomes]
rs72960240	0.85[AMR][1000 genomes]
rs72960281	0.85[AMR][1000 genomes]
rs72965177	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72965181	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73837804	1.00[EUR][1000 genomes]
rs7619643	0.85[AMR][1000 genomes]
rs7647992	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7648016	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52570000-52573600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr3:52571000-52573400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:52571200-52572800	Enhancers	Spleen	Spleen
4	chr3:52571400-52594200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:52571600-52573400	Enhancers	Primary B cells from peripheral blood	blood
6	chr3:52571600-52573400	Enhancers	Fetal Thymus	thymus
7	chr3:52571600-52573400	Enhancers	Small Intestine	intestine
8	chr3:52571600-52573600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:52571600-52573600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
10	chr3:52571800-52573200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:52571800-52573400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:52571800-52573600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:52571800-52573800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:52571800-52574200	Enhancers	Primary T cells fromperipheralblood	blood
15	chr3:52572000-52573000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:52572000-52573000	Enhancers	Primary B cells from cord blood	blood
17	chr3:52572000-52573000	Enhancers	Gastric	stomach
18	chr3:52572000-52573200	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr3:52572000-52573200	Enhancers	H9 Cell Line	embryonic stem cell
20	chr3:52572000-52573400	Enhancers	Fetal Brain Male	brain
21	chr3:52572000-52573600	Enhancers	Primary hematopoietic stem cells	blood
22	chr3:52572000-52573600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr3:52572000-52573600	Enhancers	Esophagus	oesophagus
24	chr3:52572000-52573600	Genic enhancers	Fetal Muscle Leg	muscle
25	chr3:52572000-52573600	Enhancers	Placenta	Placenta
26	chr3:52572000-52573600	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr3:52572000-52574000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr3:52572200-52572800	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr3:52572200-52572800	Enhancers	Fetal Muscle Trunk	muscle
30	chr3:52572200-52573000	Enhancers	H1 Cell Line	embryonic stem cell
31	chr3:52572200-52573000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:52572200-52573200	Enhancers	Brain Germinal Matrix	brain
33	chr3:52572200-52573200	Enhancers	Brain Substantia Nigra	brain
34	chr3:52572200-52573200	Enhancers	Fetal Lung	lung
35	chr3:52572200-52573200	Enhancers	Thymus	Thymus
36	chr3:52572200-52573400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:52572200-52573400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:52572200-52573400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:52572200-52573400	Enhancers	Stomach Mucosa	stomach
40	chr3:52572200-52573600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:52572200-52573600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr3:52572200-52573600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:52572200-52573600	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr3:52572200-52573600	Enhancers	Colon Smooth Muscle	Colon
45	chr3:52572200-52573800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:52572200-52573800	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr3:52572200-52574200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:52572200-52574400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:52572200-52574600	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr3:52572200-52575200	Weak transcription	Fetal Kidney	kidney

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