Variant report

Variant	rs10225919
Chromosome Location	chr7:5238258-5238259
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:5234033..5236801-chr7:5237323..5239372,2	MCF-7	breast:
2	chr7:5237141..5239553-chr7:5249039..5250574,2	K562	blood:
3	chr7:5237402..5239149-chr7:5239370..5241892,2	K562	blood:
4	chr7:5238079..5240119-chr7:5244033..5245712,2	MCF-7	breast:
5	chr7:5234807..5238280-chr7:5245330..5248670,4	MCF-7	breast:
6	chr7:5232342..5242315-chr7:5249039..5255391,10	K562	blood:

Variant related genes	Relation type
ENSG00000157954	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10225429	1.00[AMR][1000 genomes]
rs10242373	1.00[AMR][1000 genomes]
rs10243571	1.00[AMR][1000 genomes]
rs10245417	1.00[AMR][1000 genomes]
rs10249285	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10252983	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10253380	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10270945	1.00[AMR][1000 genomes]
rs10273014	1.00[AMR][1000 genomes]
rs10279924	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28411908	1.00[AMR][1000 genomes]
rs28447119	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28450156	1.00[AMR][1000 genomes]
rs28461705	1.00[AMR][1000 genomes]
rs28545115	1.00[AMR][1000 genomes]
rs6979367	1.00[AMR][1000 genomes]
rs73316646	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1031697	chr7:4677463-5241790	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv538704	chr7:4677463-5241790	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
5	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
6	nsv1031007	chr7:5101766-5262695	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv916396	chr7:5128917-5370805	Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
9	nsv1015639	chr7:5209510-5255399	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	nsv887390	chr7:5224407-5411296	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv887391	chr7:5224407-5572132	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	292 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5231200-5239400	Weak transcription	A549	lung
2	chr7:5231200-5240200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:5231200-5249200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:5231200-5254200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:5231400-5247000	Strong transcription	Fetal Muscle Trunk	muscle
6	chr7:5231400-5253800	Weak transcription	Fetal Kidney	kidney
7	chr7:5231400-5279800	Weak transcription	Fetal Brain Male	brain
8	chr7:5231600-5238400	Weak transcription	K562	blood
9	chr7:5231600-5239200	Weak transcription	Colonic Mucosa	Colon
10	chr7:5231600-5239400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr7:5231600-5239800	Weak transcription	Fetal Brain Female	brain
12	chr7:5231600-5240000	Weak transcription	Psoas Muscle	Psoas
13	chr7:5231600-5252600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr7:5231800-5239400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr7:5231800-5241600	Weak transcription	HMEC	breast
16	chr7:5231800-5245000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:5231800-5249800	Weak transcription	Brain Angular Gyrus	brain
18	chr7:5231800-5254200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr7:5231800-5273400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:5232000-5239400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr7:5232000-5257200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr7:5232200-5239200	Weak transcription	Brain Hippocampus Middle	brain
23	chr7:5232200-5239400	Weak transcription	Colon Smooth Muscle	Colon
24	chr7:5232200-5239400	Weak transcription	Right Atrium	heart
25	chr7:5232200-5240000	Weak transcription	Right Ventricle	heart
26	chr7:5232200-5256600	Weak transcription	Small Intestine	intestine
27	chr7:5232400-5247200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:5232400-5256200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr7:5232600-5239400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr7:5232600-5254000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr7:5233000-5247200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr7:5233000-5255200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr7:5233600-5239000	Weak transcription	HSMMtube	muscle
34	chr7:5233600-5239400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr7:5233800-5238400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr7:5233800-5239200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr7:5233800-5239400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr7:5233800-5239400	Weak transcription	Aorta	Aorta
39	chr7:5233800-5239400	Weak transcription	Pancreas	Pancrea
40	chr7:5233800-5239400	Weak transcription	NHDF-Ad	bronchial
41	chr7:5233800-5239600	Weak transcription	Brain Anterior Caudate	brain
42	chr7:5233800-5242600	Weak transcription	HSMM	muscle
43	chr7:5233800-5250400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr7:5234000-5239000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr7:5234000-5239200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr7:5234000-5239200	Weak transcription	NHLF	lung
47	chr7:5234000-5246200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr7:5234000-5250400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr7:5234000-5274800	Weak transcription	Stomach Mucosa	stomach
50	chr7:5234200-5238600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links