Variant report

Variant	rs62279582
Chromosome Location	chr3:161278013-161278014
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160813469..160814648-chr3:161277747..161278407,3	MCF-7	breast:
2	chr3:161277610..161278375-chr3:161317637..161318163,2	MCF-7	breast:
3	chr3:161277802..161278537-chr3:161469868..161470746,2	MCF-7	breast:
4	chr3:161089138..161091531-chr3:161277246..161278957,3	MCF-7	breast:
5	chr3:161139368..161142098-chr3:161277561..161279557,2	MCF-7	breast:
6	chr3:161141625..161142575-chr3:161277741..161278641,2	MCF-7	breast:
7	chr3:161277599..161279410-chr3:161282056..161284601,2	MCF-7	breast:
8	chr3:161125406..161127626-chr3:161276162..161278825,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs62278296	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62278346	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62279583	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62279584	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62279586	0.83[AMR][1000 genomes]
rs62279589	0.93[EUR][1000 genomes]
rs62279591	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62279616	0.97[EUR][1000 genomes]
rs62279623	0.97[EUR][1000 genomes]
rs62279624	0.97[EUR][1000 genomes]
rs62279626	0.97[EUR][1000 genomes]
rs62279627	0.97[EUR][1000 genomes]
rs62279628	0.97[EUR][1000 genomes]
rs62279629	0.97[EUR][1000 genomes]
rs62279631	0.97[EUR][1000 genomes]
rs62279632	0.97[EUR][1000 genomes]
rs62279657	0.90[EUR][1000 genomes]
rs62281362	0.97[EUR][1000 genomes]
rs62281364	0.97[EUR][1000 genomes]
rs62281365	0.97[EUR][1000 genomes]
rs62281366	0.97[EUR][1000 genomes]
rs62281463	0.83[AMR][1000 genomes]
rs62281466	0.93[EUR][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	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
2	nsv829773	chr3:161150422-161315189	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv829774	chr3:161229405-161386919	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2422309	chr3:161242389-161425932	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv877711	chr3:161275848-161486665	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161272800-161279600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:161275800-161278200	Enhancers	NH-A	brain
3	chr3:161276600-161278400	Weak transcription	Fetal Heart	heart
4	chr3:161276800-161280400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:161277200-161278200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr3:161277600-161278200	Active TSS	Brain Angular Gyrus	brain
7	chr3:161277600-161278200	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr3:161277600-161278200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:161277600-161278200	Enhancers	HMEC	breast
10	chr3:161277600-161278400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:161277600-161278400	Flanking Active TSS	Brain Hippocampus Middle	brain
12	chr3:161277600-161278600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr3:161277600-161278600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr3:161277800-161278200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:161277800-161278200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:161277800-161278200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:161277800-161278200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:161277800-161278200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:161277800-161278200	Active TSS	Brain Substantia Nigra	brain
20	chr3:161277800-161278200	Active TSS	Fetal Kidney	kidney
21	chr3:161277800-161278200	Active TSS	A549	lung
22	chr3:161277800-161278400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:161277800-161278400	Enhancers	Brain Germinal Matrix	brain
24	chr3:161277800-161278400	Enhancers	Colon Smooth Muscle	Colon
25	chr3:161277800-161278400	Enhancers	Fetal Muscle Leg	muscle
26	chr3:161277800-161278600	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr3:161277800-161278600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr3:161278000-161278200	Active TSS	Brain Cingulate Gyrus	brain
29	chr3:161278000-161278200	Active TSS	Fetal Brain Female	brain
30	chr3:161278000-161278400	Enhancers	Adipose Nuclei	Adipose
31	chr3:161278000-161278400	Enhancers	Fetal Lung	lung
32	chr3:161278000-161278400	Enhancers	Fetal Muscle Trunk	muscle
33	chr3:161278000-161278400	Enhancers	Stomach Smooth Muscle	stomach
34	chr3:161278000-161278600	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr3:161278000-161278600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:161278000-161278600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:161278000-161278600	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr3:161278000-161280600	Weak transcription	Dnd41	blood

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