Variant report

Variant	rs3754533
Chromosome Location	chr2:152697463-152697464
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152695100..152696940-chr2:152696997..152699571,2	MCF-7	breast:
2	chr2:152688578..152690368-chr2:152697278..152699911,2	K562	blood:
3	chr2:152684800..152686685-chr2:152697189..152699258,3	K562	blood:

Variant related genes	Relation type
ENSG00000162980	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12624108	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs16830417	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3754534	1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3768654	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4077123	1.00[EUR][1000 genomes]
rs59269531	1.00[EUR][1000 genomes]
rs72621646	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72621647	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72621648	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72621649	1.00[AMR][1000 genomes];1.00[EUR][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	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv1010582	chr2:152692238-152701782	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152685600-152697600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:152685600-152699400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:152685600-152709600	Weak transcription	Fetal Brain Female	brain
4	chr2:152685800-152699200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:152685800-152699400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:152685800-152702200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:152688000-152697600	Weak transcription	HepG2	liver
8	chr2:152694600-152698800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:152694600-152699400	Weak transcription	Brain Substantia Nigra	brain
10	chr2:152694800-152699200	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:152695000-152732600	Weak transcription	Brain Angular Gyrus	brain
12	chr2:152695200-152698200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:152695600-152698400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:152695600-152700400	Weak transcription	Fetal Brain Male	brain
15	chr2:152695800-152701600	Weak transcription	Esophagus	oesophagus
16	chr2:152696000-152699200	Weak transcription	Brain Anterior Caudate	brain
17	chr2:152696200-152699600	Weak transcription	Fetal Thymus	thymus
18	chr2:152696400-152698000	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr2:152696600-152697800	Flanking Active TSS	GM12878-XiMat	blood
20	chr2:152696600-152698200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr2:152696800-152697600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:152696800-152697600	Enhancers	Brain Germinal Matrix	brain
23	chr2:152696800-152697600	Enhancers	Duodenum Mucosa	Duodenum
24	chr2:152697200-152697800	Enhancers	Fetal Intestine Small	intestine
25	chr2:152697200-152698800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:152697200-152700600	Weak transcription	Fetal Lung	lung
27	chr2:152697400-152697600	Enhancers	Fetal Heart	heart
28	chr2:152697400-152697600	Active TSS	Gastric	stomach
29	chr2:152697400-152698200	Strong transcription	Fetal Muscle Leg	muscle
30	chr2:152697400-152699600	Weak transcription	Primary B cells from peripheral blood	blood

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