Variant report

Variant	rs4852902
Chromosome Location	chr2:73090001-73090002
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:73089617..73090286-chr20:55819429..55820102,2	MCF-7	breast:
2	chr2:73089395..73090340-chr2:73161832..73162679,3	K562	blood:
3	chr2:72997801..72998975-chr2:73089049..73090244,9	MCF-7	breast:
4	chr2:73089411..73090326-chr2:73404255..73404960,4	K562	blood:
5	chr2:73089438..73090336-chr2:73439331..73440047,4	MCF-7	breast:
6	chr2:73087670..73090180-chr2:73094273..73097260,2	K562	blood:
7	chr2:72997697..72998629-chr2:73089302..73090282,5	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10211019	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1027848	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496186	0.92[CEU][hapmap]
rs10865393	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126385	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1150500	1.00[CEU][hapmap]
rs1161265	1.00[CEU][hapmap]
rs1161267	1.00[CEU][hapmap]
rs11684985	0.85[CEU][hapmap]
rs11894160	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12474728	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622275	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12713775	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12989141	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12996406	0.92[CEU][hapmap]
rs13035731	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567230	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995734	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2048170	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048171	0.92[CEU][hapmap]
rs2135985	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420880	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420881	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420883	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2421095	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4321391	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852298	0.91[CEU][hapmap]
rs4852893	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6546782	0.92[CEU][hapmap]
rs6546783	0.92[CEU][hapmap]
rs6546786	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546788	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546789	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546790	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546791	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546792	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730083	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6739002	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6750740	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6758431	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758542	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7571064	0.84[CEU][hapmap]
rs7580268	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs7586787	0.94[EUR][1000 genomes]
rs7588602	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7592155	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs925146	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925147	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925148	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990569	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834259	chr2:72941118-73114106	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv532723	chr2:73088191-73219259	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4852902	CYP26B1	cis	Whole Blood	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73089200-73090200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
2	chr2:73089200-73090200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
3	chr2:73089200-73090400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:73089200-73090400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
5	chr2:73089200-73090400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:73089200-73090400	Active TSS	Brain Angular Gyrus	brain
7	chr2:73089200-73090400	Flanking Active TSS	Brain Anterior Caudate	brain
8	chr2:73089200-73090400	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr2:73089200-73090400	Flanking Active TSS	Hela-S3	cervix
10	chr2:73089200-73090600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr2:73089400-73090200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:73089400-73090200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:73089400-73090200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
14	chr2:73089400-73090200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
15	chr2:73089400-73090200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
16	chr2:73089400-73090200	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr2:73089400-73090200	Active TSS	Brain Cingulate Gyrus	brain
18	chr2:73089400-73090200	Bivalent Enhancer	Fetal Muscle Leg	muscle
19	chr2:73089400-73090200	Bivalent Enhancer	Placenta	Placenta
20	chr2:73089400-73090200	Active TSS	Right Atrium	heart
21	chr2:73089400-73090200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
22	chr2:73089400-73090200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
23	chr2:73089400-73090200	Bivalent Enhancer	Stomach Mucosa	stomach
24	chr2:73089400-73090200	Enhancers	Spleen	Spleen
25	chr2:73089400-73090200	Flanking Active TSS	GM12878-XiMat	blood
26	chr2:73089400-73090200	Flanking Active TSS	HMEC	breast
27	chr2:73089400-73090200	Bivalent/Poised TSS	HSMMtube	muscle
28	chr2:73089400-73090400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:73089400-73090400	Active TSS	H9 Cell Line	embryonic stem cell
30	chr2:73089400-73090400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:73089400-73090400	Enhancers	Left Ventricle	heart
32	chr2:73089600-73090200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:73089600-73090200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:73089600-73090200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr2:73089600-73090200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:73089600-73090200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:73089600-73090200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:73089600-73090200	Active TSS	Colon Smooth Muscle	Colon
39	chr2:73089600-73090200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
40	chr2:73089600-73090200	Bivalent Enhancer	Fetal Lung	lung
41	chr2:73089600-73090200	Bivalent Enhancer	Fetal Stomach	stomach
42	chr2:73089600-73090200	Bivalent Enhancer	Fetal Thymus	thymus
43	chr2:73089600-73090200	Enhancers	Lung	lung
44	chr2:73089600-73090200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
45	chr2:73089600-73090200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
46	chr2:73089600-73090400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr2:73089600-73090400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:73089600-73090400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:73089600-73090400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:73089600-73090400	Bivalent Enhancer	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links