Variant report

Variant	rs6439466
Chromosome Location	chr3:133896641-133896642
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	chr3:133894692..133896687-chr3:134204158..134205758,2	MCF-7	breast:
2	chr3:133896485..133899464-chr3:133905118..133906997,2	K562	blood:

Variant related genes	Relation type
ENSG00000129055	Chromatin interaction
ENSG00000182923	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10935104	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs1131262	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11707763	0.83[ASN][1000 genomes]
rs11915143	0.83[ASN][1000 genomes]
rs35322473	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3890774	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4072180	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4324466	0.94[ASN][1000 genomes]
rs4682664	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682666	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682668	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682669	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56073423	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6650893	0.84[ASN][1000 genomes]
rs6762690	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776502	0.91[CEU][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6780295	0.84[ASN][1000 genomes]
rs6800143	0.94[ASN][1000 genomes]
rs6808085	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7355922	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7609611	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7622046	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9283588	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9812461	0.90[ASN][1000 genomes]
rs9818714	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9823873	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9825808	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9827728	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9832732	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9839819	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9853568	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9856298	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9856792	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9858069	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9858450	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9858707	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133863000-133902200	Weak transcription	GM12878-XiMat	blood
2	chr3:133864200-133899800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:133866200-133898600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:133871800-133919200	Weak transcription	K562	blood
5	chr3:133873400-133907400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:133874400-133929400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:133874600-133933600	Weak transcription	Colonic Mucosa	Colon
8	chr3:133877600-133907400	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:133877600-133935200	Weak transcription	Psoas Muscle	Psoas
10	chr3:133877800-133920200	Weak transcription	Brain Substantia Nigra	brain
11	chr3:133877800-133950200	Weak transcription	Small Intestine	intestine
12	chr3:133878200-133901600	Weak transcription	Fetal Brain Male	brain
13	chr3:133878400-133907400	Weak transcription	Brain Angular Gyrus	brain
14	chr3:133881800-133908800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:133882400-133897400	Weak transcription	Fetal Kidney	kidney
16	chr3:133884600-133900000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:133885000-133902400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:133885600-133897800	Weak transcription	A549	lung
19	chr3:133885600-133907400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:133885600-133919600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr3:133887200-133897000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:133887600-133900400	Strong transcription	Primary T cells from cord blood	blood
23	chr3:133887600-133902800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:133887600-133903400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:133887800-133897400	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr3:133887800-133900800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:133887800-133900800	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr3:133888000-133901000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:133888400-133923600	Weak transcription	Fetal Heart	heart
30	chr3:133888600-133905400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:133891200-133896800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:133891400-133900600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:133893200-133907200	Weak transcription	Brain Anterior Caudate	brain
34	chr3:133893200-133917400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:133893400-133898200	Weak transcription	NHLF	lung
36	chr3:133894000-133898400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:133894400-133912600	Weak transcription	Fetal Thymus	thymus
38	chr3:133894800-133898000	Weak transcription	Fetal Brain Female	brain
39	chr3:133894800-133898200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr3:133894800-133898200	Weak transcription	Fetal Lung	lung
41	chr3:133894800-133898200	Weak transcription	Ovary	ovary
42	chr3:133894800-133898200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr3:133894800-133898200	Weak transcription	HSMMtube	muscle
44	chr3:133894800-133898800	Weak transcription	HSMM	muscle
45	chr3:133894800-133907200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:133894800-133912600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr3:133894800-133917800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:133894800-133917800	Weak transcription	Right Ventricle	heart
49	chr3:133894800-133917800	Weak transcription	Thymus	Thymus
50	chr3:133894800-133935200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links