Variant report

Variant	rs336559
Chromosome Location	chr3:161133966-161133967
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160786404..160789728-chr3:161132273..161134989,3	MCF-7	breast:
2	chr3:161003253..161016100-chr3:161121496..161137189,33	MCF-7	breast:
3	chr3:160821926..160824694-chr3:161130720..161134424,3	MCF-7	breast:
4	chr12:53441527..53442038-chr3:161133367..161134304,2	Hela-S3	cervix:
5	chr3:160934874..160951087-chr3:161118055..161142485,77	MCF-7	breast:
6	chr3:160937705..160941241-chr3:161127569..161134417,11	MCF-7	breast:
7	chr17:59472839..59476239-chr3:161133074..161135554,3	MCF-7	breast:
8	chr3:161040559..161042979-chr3:161133154..161135842,2	MCF-7	breast:
9	chr3:161007555..161015806-chr3:161127103..161142651,19	MCF-7	breast:
10	chr3:102426713..102428233-chr3:161131598..161134258,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000169251	Chromatin interaction
ENSG00000169255	Chromatin interaction
ENSG00000271052	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs163136	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs336552	0.84[ASN][1000 genomes]
rs336556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336560	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs336588	1.00[YRI][hapmap]
rs339111	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs339124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420081	0.95[ASN][1000 genomes]
rs457240	0.95[ASN][1000 genomes]
rs459679	0.95[ASN][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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	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
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv877710	chr3:161087857-161245414	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161125600-161137000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:161128200-161134000	Weak transcription	Esophagus	oesophagus
3	chr3:161129600-161134600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr3:161130600-161134800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:161131600-161134000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:161131600-161134000	Weak transcription	Right Atrium	heart
7	chr3:161131600-161134200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:161131600-161140000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:161131800-161134000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:161131800-161134000	Weak transcription	Aorta	Aorta
11	chr3:161131800-161134000	Weak transcription	Brain Angular Gyrus	brain
12	chr3:161131800-161134000	Weak transcription	Pancreas	Pancrea
13	chr3:161131800-161134000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:161131800-161134200	Weak transcription	Left Ventricle	heart
15	chr3:161131800-161134200	Weak transcription	NHLF	lung
16	chr3:161132400-161134000	Enhancers	NH-A	brain
17	chr3:161132400-161134400	Enhancers	Adipose Nuclei	Adipose
18	chr3:161132400-161134600	Enhancers	Stomach Mucosa	stomach
19	chr3:161132800-161134000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:161132800-161134000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:161132800-161134000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:161132800-161134200	Enhancers	Hela-S3	cervix
23	chr3:161132800-161134600	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr3:161132800-161134600	Enhancers	NHDF-Ad	bronchial
25	chr3:161133000-161134600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr3:161133200-161134200	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr3:161133200-161134400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr3:161133200-161134600	Enhancers	Liver	Liver
29	chr3:161133200-161134600	Enhancers	HMEC	breast
30	chr3:161133200-161134600	Enhancers	NHEK	skin
31	chr3:161133400-161134400	Enhancers	Brain Hippocampus Middle	brain
32	chr3:161133400-161134400	Enhancers	Fetal Lung	lung
33	chr3:161133400-161134400	Enhancers	Stomach Smooth Muscle	stomach
34	chr3:161133400-161134400	Flanking Active TSS	HUVEC	blood vessel
35	chr3:161133400-161134600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:161133400-161134600	Flanking Active TSS	A549	lung
37	chr3:161133600-161134200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:161133600-161134200	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr3:161133600-161134200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:161133600-161134200	Enhancers	HepG2	liver
41	chr3:161133600-161134400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:161133600-161134400	Enhancers	Brain Cingulate Gyrus	brain
43	chr3:161133600-161134400	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr3:161133600-161134400	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr3:161133600-161134600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:161133600-161134600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:161133800-161134000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:161133800-161134000	Enhancers	Osteobl	bone
49	chr3:161133800-161134400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:161133800-161134400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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