Variant report

Variant	rs11264302
Chromosome Location	chr1:155028522-155028523
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154954733..154957486-chr1:155027270..155029022,2	MCF-7	breast:
2	chr1:155013927..155032770-chr1:155044175..155061131,53	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143590	Chromatin interaction
ENSG00000160688	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10158328	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1061122	1.00[JPT][hapmap]
rs11264303	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582128	1.00[JPT][hapmap]
rs1218584	1.00[JPT][hapmap]
rs1218585	1.00[JPT][hapmap]
rs1218587	1.00[JPT][hapmap]
rs1218589	1.00[JPT][hapmap]
rs1611770	1.00[JPT][hapmap]
rs4845397	1.00[JPT][hapmap]
rs4845402	1.00[JPT][hapmap]
rs6660884	1.00[JPT][hapmap];0.83[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	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
3	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
4	nsv872455	chr1:155003954-155106550	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
5	nsv524157	chr1:155026942-155030557	Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11264302	S100A3	cis	parietal	SCAN
rs11264302	PI4KB	cis	parietal	SCAN
rs11264302	JTB	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155025000-155034200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:155025200-155028600	Weak transcription	Brain Angular Gyrus	brain
3	chr1:155025200-155028600	Weak transcription	Small Intestine	intestine
4	chr1:155025200-155034000	Weak transcription	NH-A	brain
5	chr1:155025200-155034200	Weak transcription	Psoas Muscle	Psoas
6	chr1:155025200-155034200	Weak transcription	NHDF-Ad	bronchial
7	chr1:155025400-155028600	Weak transcription	HepG2	liver
8	chr1:155025400-155028800	Weak transcription	Brain Germinal Matrix	brain
9	chr1:155025400-155029000	Weak transcription	Fetal Brain Female	brain
10	chr1:155025400-155034000	Weak transcription	GM12878-XiMat	blood
11	chr1:155025600-155028600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:155025600-155028600	Weak transcription	Stomach Mucosa	stomach
13	chr1:155025600-155030400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:155025600-155033800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:155025600-155034200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:155025800-155031400	Strong transcription	Fetal Intestine Small	intestine
17	chr1:155025800-155031800	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr1:155025800-155033600	Strong transcription	A549	lung
19	chr1:155025800-155034000	Strong transcription	Brain Cingulate Gyrus	brain
20	chr1:155026000-155029400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:155026000-155030800	Weak transcription	K562	blood
22	chr1:155026000-155033200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:155026000-155033600	Strong transcription	Brain Substantia Nigra	brain
24	chr1:155026000-155033800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr1:155026000-155033800	Strong transcription	Fetal Stomach	stomach
26	chr1:155026000-155034200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:155026000-155034200	Weak transcription	Right Atrium	heart
28	chr1:155026200-155029200	Strong transcription	Right Ventricle	heart
29	chr1:155026200-155029600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:155026200-155029600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:155026200-155032600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr1:155026200-155033000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:155026200-155033200	Strong transcription	Duodenum Mucosa	Duodenum
34	chr1:155026200-155033400	Strong transcription	HMEC	breast
35	chr1:155026200-155033600	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:155026200-155033600	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr1:155026200-155033800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr1:155026200-155033800	Weak transcription	Primary B cells from cord blood	blood
39	chr1:155026200-155033800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr1:155026200-155034000	Weak transcription	Fetal Lung	lung
41	chr1:155026200-155034200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:155026400-155028600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:155026400-155031600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:155026400-155031600	Strong transcription	Hela-S3	cervix
45	chr1:155026400-155032600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:155026400-155033200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:155026400-155033400	Strong transcription	Gastric	stomach
48	chr1:155026400-155033400	Strong transcription	Stomach Smooth Muscle	stomach
49	chr1:155026400-155033600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:155026400-155033600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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