Variant report

Variant	rs4253234
Chromosome Location	chr10:50666482-50666483
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:50664489..50667007-chr10:50746262..50748316,2	MCF-7	breast:
2	chr10:50656731..50658500-chr10:50666252..50669153,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225830	Chromatin interaction
ENSG00000258838	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10776575	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10857497	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10857504	0.88[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10857506	0.84[EUR][1000 genomes]
rs10857510	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11101144	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11101155	0.84[EUR][1000 genomes]
rs11591393	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12146288	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1917821	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2177819	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2229760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2281792	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2281793	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2377900	0.84[EUR][1000 genomes]
rs3750747	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3793784	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4253038	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4253160	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4253190	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7895633	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7898545	0.80[EUR][1000 genomes]
rs9988727	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][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	nsv895377	chr10:50588990-50678212	ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50656600-50672600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:50660000-50666800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr10:50660400-50672400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr10:50662000-50669800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr10:50662200-50669600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr10:50662200-50669600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr10:50662200-50669600	Strong transcription	Left Ventricle	heart
8	chr10:50662200-50669800	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr10:50662200-50677800	Weak transcription	Fetal Heart	heart
10	chr10:50662200-50691600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr10:50662400-50667000	Weak transcription	Psoas Muscle	Psoas
12	chr10:50662400-50690000	Weak transcription	Stomach Mucosa	stomach
13	chr10:50662400-50693200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr10:50662600-50666600	Weak transcription	Brain Germinal Matrix	brain
15	chr10:50662600-50667000	Weak transcription	Brain Hippocampus Middle	brain
16	chr10:50662600-50669600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr10:50662600-50669600	Strong transcription	Duodenum Mucosa	Duodenum
18	chr10:50662600-50670200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr10:50662600-50670400	Strong transcription	Osteobl	bone
20	chr10:50662600-50674800	Weak transcription	Colonic Mucosa	Colon
21	chr10:50662600-50676600	Weak transcription	Small Intestine	intestine
22	chr10:50662600-50677600	Weak transcription	NHDF-Ad	bronchial
23	chr10:50662600-50691400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr10:50662800-50666800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr10:50662800-50666800	Weak transcription	GM12878-XiMat	blood
26	chr10:50662800-50667000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr10:50662800-50667000	Weak transcription	Brain Angular Gyrus	brain
28	chr10:50662800-50667800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr10:50663000-50666600	Weak transcription	Primary B cells from cord blood	blood
30	chr10:50663000-50669400	Strong transcription	Stomach Smooth Muscle	stomach
31	chr10:50663000-50669600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr10:50663000-50675800	Weak transcription	Colon Smooth Muscle	Colon
33	chr10:50663200-50669600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr10:50663200-50672600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr10:50663200-50693800	Weak transcription	HepG2	liver
36	chr10:50663400-50669600	Strong transcription	Brain Anterior Caudate	brain
37	chr10:50663400-50669600	Strong transcription	Fetal Muscle Leg	muscle
38	chr10:50663400-50669800	Strong transcription	HUVEC	blood vessel
39	chr10:50663400-50671200	Strong transcription	HMEC	breast
40	chr10:50663600-50669600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr10:50663600-50669600	Strong transcription	Liver	Liver
42	chr10:50663600-50669600	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr10:50663600-50671000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr10:50663600-50671000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr10:50663800-50667000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr10:50663800-50669600	Strong transcription	Primary B cells from peripheral blood	blood
47	chr10:50663800-50669600	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr10:50663800-50669600	Strong transcription	Right Ventricle	heart
49	chr10:50663800-50669800	Strong transcription	Primary T cells from cord blood	blood
50	chr10:50663800-50669800	Strong transcription	Adipose Nuclei	Adipose

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