Variant report

Variant	rs4253069
Chromosome Location	chr10:50726593-50726594
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr10:50726580-50726730	HBMEC	blood vessel:	n/a	n/a
2	CTCF	chr10:50726393-50727672	A549	lung:	n/a	chr10:50727223-50727236 chr10:50727221-50727239
3	POLR2A	chr10:50726057-50726873	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:50726583..50728092-chr10:50732083..50734256,2	MCF-7	breast:
2	chr10:50726029..50728979-chr10:50731581..50735350,6	K562	blood:
3	chr10:50724821..50729589-chr10:50731335..50734731,5	K562	blood:
4	chr10:50715569..50718101-chr10:50726217..50728314,2	K562	blood:
5	chr10:50712711..50715456-chr10:50724740..50726788,2	K562	blood:
6	chr10:50726159..50727907-chr10:50745055..50747037,2	MCF-7	breast:

Variant related genes	Relation type
PGBD3	TF binding region
ENSG00000243251	Chromatin interaction
ENSG00000225830	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11101177	0.85[AMR][1000 genomes]
rs2228525	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4253010	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4253029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4253050	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4253061	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4253102	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs4253109	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4253112	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4253133	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4253151	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4253225	1.00[AMR][1000 genomes]
rs4838511	0.85[AMR][1000 genomes]
rs4838531	1.00[AMR][1000 genomes]
rs57865789	0.87[AMR][1000 genomes]
rs60749172	0.87[AMR][1000 genomes]
rs73311046	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73315042	0.87[AMR][1000 genomes]
rs73315047	0.87[AMR][1000 genomes]
rs73315061	0.87[AMR][1000 genomes]
rs73315065	0.87[AMR][1000 genomes]
rs73315077	0.87[AMR][1000 genomes]
rs73315085	0.87[AMR][1000 genomes]
rs73315096	0.87[AMR][1000 genomes]
rs73316905	0.87[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	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv831867	chr10:50607857-50788751	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv3346476	chr10:50610853-50987802	Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3385048	chr10:50610942-50988537	Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1051636	chr10:50675292-50732280	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50686600-50727600	Weak transcription	Fetal Brain Male	brain
2	chr10:50686600-50731000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr10:50690200-50728200	Weak transcription	Colonic Mucosa	Colon
4	chr10:50691000-50728200	Weak transcription	Gastric	stomach
5	chr10:50691600-50728400	Weak transcription	Fetal Kidney	kidney
6	chr10:50696400-50731800	Weak transcription	Small Intestine	intestine
7	chr10:50706400-50726600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr10:50707000-50732200	Weak transcription	NHDF-Ad	bronchial
9	chr10:50707600-50735600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr10:50711600-50727800	Weak transcription	Right Atrium	heart
11	chr10:50715000-50732200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr10:50715800-50727800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr10:50716200-50731000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr10:50716800-50726600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr10:50717000-50727400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr10:50717200-50729400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr10:50717200-50731200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr10:50717200-50736200	Weak transcription	Colon Smooth Muscle	Colon
19	chr10:50717200-50746000	Weak transcription	Fetal Heart	heart
20	chr10:50717400-50737000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr10:50717600-50730600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr10:50717600-50731600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr10:50718200-50729200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr10:50718600-50726600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr10:50718600-50726600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr10:50718800-50726600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr10:50718800-50727600	Weak transcription	Brain Angular Gyrus	brain
28	chr10:50718800-50727800	Weak transcription	Esophagus	oesophagus
29	chr10:50720000-50728200	Weak transcription	Fetal Thymus	thymus
30	chr10:50720400-50746200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr10:50720600-50727000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr10:50721000-50726800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr10:50721000-50728000	Weak transcription	Thymus	Thymus
34	chr10:50721600-50734800	Weak transcription	A549	lung
35	chr10:50721800-50730000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr10:50722200-50728000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr10:50722400-50727000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr10:50722800-50727200	Strong transcription	HUVEC	blood vessel
39	chr10:50723000-50729800	Strong transcription	Duodenum Mucosa	Duodenum
40	chr10:50723000-50730000	Strong transcription	Primary B cells from peripheral blood	blood
41	chr10:50723000-50730000	Strong transcription	Primary hematopoietic stem cells	blood
42	chr10:50723000-50734400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr10:50723000-50741000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr10:50723200-50726600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr10:50723200-50727800	Strong transcription	Hela-S3	cervix
46	chr10:50723200-50741000	Strong transcription	Primary T cells from cord blood	blood
47	chr10:50723200-50741000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr10:50723200-50741000	Strong transcription	HMEC	breast
49	chr10:50723200-50741800	Strong transcription	Osteobl	bone
50	chr10:50723400-50726600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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