Variant report

Variant	rs66530305
Chromosome Location	chr3:52072084-52072085
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52071455..52074852-chr3:52088156..52091655,5	MCF-7	breast:
2	chr3:52069883..52072776-chr3:52161086..52163454,2	K562	blood:
3	chr3:52071945..52074721-chr3:52081198..52083628,2	K562	blood:

Variant related genes	Relation type
ENSG00000164086	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12485855	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12487108	0.80[AMR][1000 genomes]
rs12489539	0.83[AMR][1000 genomes]
rs12492696	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12493204	0.83[AMR][1000 genomes]
rs13096104	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17051963	0.80[AMR][1000 genomes]
rs2334959	0.91[AMR][1000 genomes]
rs2334960	0.89[AMR][1000 genomes]
rs3821841	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4687606	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4687609	0.81[AMR][1000 genomes]
rs4687798	0.91[AMR][1000 genomes]
rs4687799	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4687801	0.85[AMR][1000 genomes]
rs4687802	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4687806	0.80[AMR][1000 genomes]
rs6792935	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72622936	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72622937	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs745618	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7618573	0.83[AMR][1000 genomes]
rs7642881	0.84[AMR][1000 genomes]
rs920160	0.81[AMR][1000 genomes]
rs9848727	0.85[AMR][1000 genomes]
rs9866081	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
9	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	esv1792042	chr3:52070955-52091254	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
12	esv1793040	chr3:52070955-52091254	Active TSS Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
13	esv1797975	chr3:52070955-52091254	Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
14	esv1798814	chr3:52070955-52091254	Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
15	esv1797189	chr3:52070955-52101799	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
16	esv1798365	chr3:52070955-52101799	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52050600-52073400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:52062200-52073800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:52063600-52072400	Weak transcription	HSMM	muscle
4	chr3:52064400-52073600	Weak transcription	Spleen	Spleen
5	chr3:52066400-52073600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:52067200-52072400	Weak transcription	Fetal Brain Female	brain
7	chr3:52067400-52073400	Weak transcription	Left Ventricle	heart
8	chr3:52067600-52072600	Weak transcription	Fetal Brain Male	brain
9	chr3:52067600-52072600	Weak transcription	Right Atrium	heart
10	chr3:52067600-52073600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:52067600-52073800	Weak transcription	Brain Germinal Matrix	brain
12	chr3:52067800-52072800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:52068600-52074000	Weak transcription	Liver	Liver
14	chr3:52068800-52073600	Enhancers	HepG2	liver
15	chr3:52069200-52072200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:52069600-52075000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:52069600-52075800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:52069600-52076200	Enhancers	Brain Angular Gyrus	brain
19	chr3:52070000-52076200	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr3:52070200-52073600	Enhancers	NHEK	skin
21	chr3:52070200-52076200	Enhancers	Brain Cingulate Gyrus	brain
22	chr3:52070200-52076400	Enhancers	Brain Anterior Caudate	brain
23	chr3:52070800-52076200	Enhancers	Brain Hippocampus Middle	brain
24	chr3:52070800-52076200	Enhancers	Brain Substantia Nigra	brain
25	chr3:52071200-52075800	Enhancers	Fetal Muscle Leg	muscle
26	chr3:52071200-52075800	Enhancers	HMEC	breast
27	chr3:52071200-52079600	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:52071400-52072400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:52071400-52074200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:52071600-52072400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr3:52071600-52075400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:52071600-52079400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:52071600-52080000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:52071800-52072400	Weak transcription	Hela-S3	cervix
35	chr3:52071800-52072600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:52071800-52072600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:52071800-52072800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:52071800-52074000	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr3:52071800-52074800	Enhancers	Esophagus	oesophagus
40	chr3:52071800-52075400	Enhancers	Right Ventricle	heart
41	chr3:52071800-52075800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:52071800-52079400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:52072000-52072200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:52072000-52072800	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links