Variant report

Variant	rs6445561
Chromosome Location	chr3:53153193-53153194
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53078388..53080393-chr3:53151497..53153388,2	K562	blood:
2	chr3:53150117..53153813-chr3:53191442..53194922,3	MCF-7	breast:
3	chr3:53151107..53153969-chr3:53231326..53234111,2	K562	blood:
4	chr3:53151215..53153381-chr3:53193780..53196967,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163935	Chromatin interaction
ENSG00000163932	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11714704	1.00[AMR][1000 genomes]
rs11718387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1560331	1.00[AFR][1000 genomes]
rs2059966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4234641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4687702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4687703	0.93[AFR][1000 genomes]
rs4687704	1.00[AFR][1000 genomes]
rs4687705	1.00[AFR][1000 genomes]
rs6445562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7626998	1.00[AMR][1000 genomes]
rs7647567	1.00[AMR][1000 genomes]
rs9852564	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv590356	chr3:53134098-53170500	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	nsv460553	chr3:53147576-53185061	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	nsv590357	chr3:53147576-53185061	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
4	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 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	chr3:53119000-53154200	Weak transcription	Stomach Mucosa	stomach
2	chr3:53127000-53154200	Weak transcription	Right Atrium	heart
3	chr3:53137400-53161600	Strong transcription	Fetal Intestine Small	intestine
4	chr3:53139200-53157400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:53142800-53161000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:53145000-53161400	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:53145800-53161200	Strong transcription	Primary hematopoietic stem cells	blood
8	chr3:53147200-53160000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:53147600-53160800	Strong transcription	Fetal Muscle Trunk	muscle
10	chr3:53148000-53156200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:53148000-53163600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:53148200-53160000	Strong transcription	Brain Inferior Temporal Lobe	brain
13	chr3:53148200-53160000	Strong transcription	Duodenum Mucosa	Duodenum
14	chr3:53148200-53160000	Strong transcription	Spleen	Spleen
15	chr3:53148200-53160600	Strong transcription	Fetal Intestine Large	intestine
16	chr3:53148200-53161000	Strong transcription	Fetal Thymus	thymus
17	chr3:53148400-53153200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:53148400-53160000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:53148400-53160000	Strong transcription	Fetal Stomach	stomach
20	chr3:53148400-53160200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:53148400-53160400	Strong transcription	Primary B cells from peripheral blood	blood
22	chr3:53148400-53160800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr3:53148400-53161000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:53148400-53161000	Strong transcription	Fetal Muscle Leg	muscle
25	chr3:53148400-53161200	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:53148400-53161200	Strong transcription	Dnd41	blood
27	chr3:53148400-53161600	Strong transcription	Primary T cells from cord blood	blood
28	chr3:53148400-53163400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:53148600-53154200	Weak transcription	Fetal Heart	heart
30	chr3:53148600-53156400	Strong transcription	Adipose Nuclei	Adipose
31	chr3:53148600-53160200	Strong transcription	Brain Hippocampus Middle	brain
32	chr3:53148600-53160200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr3:53148600-53160400	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:53148600-53160800	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:53148600-53161200	Strong transcription	Liver	Liver
36	chr3:53148800-53160000	Strong transcription	Colon Smooth Muscle	Colon
37	chr3:53148800-53160200	Strong transcription	Fetal Lung	lung
38	chr3:53148800-53160400	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:53148800-53161200	Strong transcription	Stomach Smooth Muscle	stomach
40	chr3:53149200-53160000	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:53149200-53160400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:53149200-53161200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:53149400-53160000	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr3:53149400-53160200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:53149400-53160200	Strong transcription	Fetal Brain Female	brain
46	chr3:53149400-53160400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:53149400-53160400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:53149600-53160000	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr3:53149600-53161400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:53149600-53162400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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