Variant report

Variant	rs59643945
Chromosome Location	chr3:48664473-48664474
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48663872..48666244-chr3:48699915..48701423,2	K562	blood:
2	chr3:48662117..48664677-chr3:48670615..48672606,2	K562	blood:
3	chr3:48662608..48665398-chr3:48666454..48668289,2	K562	blood:

Variant related genes	Relation type
ENSG00000008300	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000225697	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1387005	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs55807958	1.00[EUR][1000 genomes]
rs60028595	1.00[EUR][1000 genomes]
rs61368683	0.81[AMR][1000 genomes]
rs6800132	0.89[AFR][1000 genomes]
rs9833600	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9839959	0.82[AMR][1000 genomes]
rs9866124	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48649000-48672000	Weak transcription	Fetal Brain Male	brain
2	chr3:48656400-48671400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:48657200-48664600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:48657800-48670000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:48658200-48668000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:48659000-48671200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:48660000-48671200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:48660400-48665000	Weak transcription	NHDF-Ad	bronchial
9	chr3:48660400-48667800	Weak transcription	A549	lung
10	chr3:48660800-48668600	Weak transcription	Fetal Lung	lung
11	chr3:48661000-48671200	Strong transcription	Aorta	Aorta
12	chr3:48661000-48671600	Weak transcription	Psoas Muscle	Psoas
13	chr3:48661200-48670200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:48661200-48670800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:48661200-48671000	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr3:48661200-48671800	Weak transcription	Small Intestine	intestine
17	chr3:48661600-48670600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:48661600-48670800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:48661600-48670800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:48661600-48670800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:48661600-48670800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr3:48661600-48670800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr3:48661600-48671200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:48661600-48671400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:48661800-48665000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:48661800-48667400	Strong transcription	Placenta	Placenta
27	chr3:48661800-48670200	Strong transcription	Spleen	Spleen
28	chr3:48661800-48670800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:48661800-48671000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:48661800-48671400	Strong transcription	NHEK	skin
31	chr3:48661800-48671600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:48662000-48666600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:48662000-48669400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:48662000-48671000	Strong transcription	Brain Hippocampus Middle	brain
35	chr3:48662000-48671000	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:48662000-48671200	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr3:48662000-48671200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:48662000-48671400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:48662000-48671400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr3:48662000-48671800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr3:48662200-48665000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr3:48662200-48670200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr3:48662200-48670600	Strong transcription	Osteobl	bone
44	chr3:48662200-48670800	Strong transcription	Thymus	Thymus
45	chr3:48662200-48671000	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:48662200-48671200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:48662200-48671200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:48662200-48671400	Strong transcription	Fetal Intestine Small	intestine
49	chr3:48662200-48671400	Strong transcription	Fetal Stomach	stomach
50	chr3:48662200-48671800	Weak transcription	Primary B cells from cord blood	blood

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