Variant report

Variant	rs60234882
Chromosome Location	chr3:49826442-49826443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49824316..49827108-chr3:49830992..49833556,2	MCF-7	breast:
2	chr3:49825629..49827827-chr3:49829411..49832341,3	K562	blood:
3	chr3:49822510..49825431-chr3:49825624..49828920,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176095	Chromatin interaction
ENSG00000187492	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12107386	1.00[AMR][1000 genomes]
rs17050905	1.00[AMR][1000 genomes]
rs28424211	1.00[AMR][1000 genomes]
rs55750059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56263643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56297242	1.00[AMR][1000 genomes]
rs57347154	1.00[AMR][1000 genomes]
rs58095278	1.00[AMR][1000 genomes]
rs58363428	1.00[AMR][1000 genomes]
rs58688714	1.00[AMR][1000 genomes]
rs59822920	1.00[AMR][1000 genomes]
rs60065407	1.00[AMR][1000 genomes]
rs60844685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61435065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832783	1.00[AMR][1000 genomes]
rs73832789	1.00[AMR][1000 genomes]
rs73832800	1.00[AMR][1000 genomes]
rs73834118	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834119	1.00[AMR][1000 genomes]
rs73834120	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834125	1.00[AMR][1000 genomes]
rs73834127	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49824600-49827200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:49824600-49828200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:49824600-49829000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:49824600-49832400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:49824800-49827200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:49824800-49827200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:49824800-49827200	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:49824800-49827200	Weak transcription	Fetal Brain Male	brain
9	chr3:49824800-49827400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:49824800-49827400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:49824800-49827400	Weak transcription	Brain Substantia Nigra	brain
12	chr3:49824800-49827600	Weak transcription	Fetal Heart	heart
13	chr3:49824800-49827800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:49824800-49827800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:49824800-49828200	Weak transcription	NH-A	brain
16	chr3:49824800-49832600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:49825000-49827200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:49825000-49827200	Weak transcription	Primary B cells from cord blood	blood
19	chr3:49825000-49827200	Weak transcription	Primary T cells from cord blood	blood
20	chr3:49825000-49827200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr3:49825000-49827200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:49825000-49827200	Weak transcription	Thymus	Thymus
23	chr3:49825000-49827400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:49825000-49827400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:49825000-49827400	Weak transcription	Fetal Intestine Small	intestine
26	chr3:49825000-49827600	Weak transcription	HUVEC	blood vessel
27	chr3:49825200-49827200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr3:49825200-49827200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr3:49825200-49827200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:49825200-49827200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:49825200-49827200	Weak transcription	Fetal Thymus	thymus
32	chr3:49825200-49827200	Weak transcription	Dnd41	blood
33	chr3:49825200-49827200	Weak transcription	HepG2	liver
34	chr3:49825200-49827400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:49825200-49827600	Weak transcription	Stomach Mucosa	stomach
36	chr3:49825200-49827800	Weak transcription	HMEC	breast
37	chr3:49825200-49828400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:49825200-49836400	Weak transcription	Esophagus	oesophagus
39	chr3:49825400-49828400	Weak transcription	K562	blood
40	chr3:49825600-49840000	Weak transcription	Spleen	Spleen
41	chr3:49825800-49826800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:49825800-49827000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:49825800-49827200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:49825800-49827400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:49826400-49827400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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