Variant report

Variant	rs7263632
Chromosome Location	chr20:25058135-25058136
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25052320..25053946-chr20:25055898..25058573,2	MCF-7	breast:
2	chr20:25056370..25059250-chr20:25174569..25177571,3	MCF-7	breast:
3	chr20:25057289..25058975-chr20:25226619..25228863,2	MCF-7	breast:
4	chr20:25054844..25058216-chr20:25060336..25062971,3	MCF-7	breast:
5	chr20:24972184..24974531-chr20:25057258..25059368,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100994	Chromatin interaction
ENSG00000100987	Chromatin interaction
ENSG00000197586	Chromatin interaction
ENSG00000101474	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1005409	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12480307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2207633	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207635	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2387577	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4813546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813548	1.00[ASN][1000 genomes]
rs4815366	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4815367	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55651034	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56157240	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56369722	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58747756	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037013	1.00[JPT][hapmap]
rs6037014	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050300	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050304	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050306	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050308	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076315	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6083734	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6083736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083737	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083745	0.84[ASN][1000 genomes]
rs6115024	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6115037	1.00[ASN][1000 genomes]
rs61304082	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62215277	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217195	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217196	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217197	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217199	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7265721	0.80[EUR][1000 genomes]
rs7266451	1.00[CHB][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs7344824	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743017	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7263632	VSX1	cis	cerebellum	SCAN
rs7263632	ACSS1	cis	cerebellum	SCAN
rs7263632	HDHD4	cis	multi-tissue	Pritchard
rs7263632	C20orf22	cis	multi-tissue	Pritchard

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25046800-25058200	Weak transcription	Right Atrium	heart
2	chr20:25056800-25058200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr20:25056800-25058600	Enhancers	Gastric	stomach
4	chr20:25057200-25058200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr20:25057200-25058200	Enhancers	Liver	Liver
6	chr20:25057200-25058200	Enhancers	Pancreas	Pancrea
7	chr20:25057200-25058200	Enhancers	HMEC	breast
8	chr20:25057200-25058200	Bivalent Enhancer	NHEK	skin
9	chr20:25057200-25058400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr20:25057200-25058800	Bivalent Enhancer	Thymus	Thymus
11	chr20:25057200-25060600	Enhancers	Dnd41	blood
12	chr20:25057400-25058200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr20:25057400-25058200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr20:25057400-25058200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr20:25057400-25058200	Bivalent Enhancer	Left Ventricle	heart
16	chr20:25057400-25058200	Flanking Active TSS	A549	lung
17	chr20:25057400-25058400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
18	chr20:25057400-25058400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
19	chr20:25057400-25058600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
20	chr20:25057400-25058800	Enhancers	Placenta	Placenta
21	chr20:25057600-25058200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr20:25057600-25058200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
23	chr20:25057600-25058200	Bivalent Enhancer	Osteobl	bone
24	chr20:25057600-25058400	Bivalent Enhancer	Stomach Mucosa	stomach
25	chr20:25057600-25058800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr20:25057600-25059000	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr20:25057800-25058200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr20:25057800-25058200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
29	chr20:25057800-25058200	Enhancers	Psoas Muscle	Psoas
30	chr20:25057800-25058400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr20:25057800-25058400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
32	chr20:25057800-25058400	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr20:25057800-25058600	Bivalent Enhancer	HSMM	muscle
34	chr20:25057800-25058800	Active TSS	Brain Angular Gyrus	brain
35	chr20:25057800-25058800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
36	chr20:25057800-25058800	Bivalent Enhancer	Lung	lung
37	chr20:25057800-25059000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr20:25058000-25058200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr20:25058000-25058200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr20:25058000-25058200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr20:25058000-25058200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr20:25058000-25058200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
43	chr20:25058000-25058200	Enhancers	Esophagus	oesophagus
44	chr20:25058000-25058200	Flanking Bivalent TSS/Enh	HepG2	liver
45	chr20:25058000-25058200	Enhancers	HSMMtube	muscle
46	chr20:25058000-25058400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
47	chr20:25058000-25058400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
48	chr20:25058000-25058600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
49	chr20:25058000-25058600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr20:25058000-25058600	Active TSS	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links