Variant report

Variant	rs72964041
Chromosome Location	chr3:52087279-52087280
allele	A/G
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	chr3:52087181..52088866-chr3:52188475..52190351,2	K562	blood:
2	chr3:52063502..52067953-chr3:52083827..52087506,5	K562	blood:
3	chr3:52026823..52031380-chr3:52087204..52091486,4	K562	blood:
4	chr3:52086989..52088161-chr3:52156846..52157770,4	MCF-7	breast:
5	chr3:51974895..51976742-chr3:52087202..52089493,2	K562	blood:
6	chr3:52085365..52087890-chr3:52105786..52108458,2	MCF-7	breast:
7	chr3:52087227..52088495-chr3:52178231..52179051,5	MCF-7	breast:
8	chr3:52086312..52088245-chr3:52101960..52104094,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162244	Chromatin interaction
ENSG00000164087	Chromatin interaction
ENSG00000114767	Chromatin interaction
ENSG00000041880	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10433611	1.00[AMR][1000 genomes]
rs2089225	1.00[AMR][1000 genomes]
rs323888	1.00[AMR][1000 genomes]
rs323899	1.00[AMR][1000 genomes]
rs323901	1.00[AMR][1000 genomes]
rs352646	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35898691	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57236484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59196507	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61333587	1.00[AMR][1000 genomes]
rs6446153	1.00[AMR][1000 genomes]
rs72955239	1.00[AMR][1000 genomes]
rs72955243	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72955259	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72955260	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72955262	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7430706	1.00[AMR][1000 genomes]
rs7612847	1.00[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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52081600-52088600	Genic enhancers	Placenta	Placenta
2	chr3:52081600-52088800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:52081800-52088200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:52082400-52088000	Strong transcription	Fetal Intestine Large	intestine
5	chr3:52082400-52088000	Genic enhancers	Spleen	Spleen
6	chr3:52082600-52088600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:52083200-52088400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:52083200-52088400	Genic enhancers	Gastric	stomach
9	chr3:52083200-52090200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:52084000-52088200	Genic enhancers	Pancreas	Pancrea
11	chr3:52084400-52088600	Genic enhancers	Placenta Amnion	Placenta Amnion
12	chr3:52084800-52088800	Transcr. at gene 5' and 3'	NHEK	skin
13	chr3:52084800-52090000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:52085000-52088600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:52085000-52089200	Enhancers	Primary B cells from peripheral blood	blood
16	chr3:52085000-52090200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:52085200-52088600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
18	chr3:52085200-52088800	Weak transcription	Small Intestine	intestine
19	chr3:52085400-52088600	Transcr. at gene 5' and 3'	Brain Angular Gyrus	brain
20	chr3:52085400-52088600	Transcr. at gene 5' and 3'	Brain Substantia Nigra	brain
21	chr3:52085400-52088800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr3:52085400-52088800	Enhancers	Stomach Mucosa	stomach
23	chr3:52085400-52089000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
24	chr3:52085600-52088400	Genic enhancers	Liver	Liver
25	chr3:52085600-52088800	Genic enhancers	Fetal Intestine Small	intestine
26	chr3:52085600-52088800	Transcr. at gene 5' and 3'	HMEC	breast
27	chr3:52085800-52087800	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr3:52085800-52088400	Transcr. at gene 5' and 3'	Brain Anterior Caudate	brain
29	chr3:52085800-52088600	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
30	chr3:52085800-52088800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
31	chr3:52085800-52088800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:52085800-52088800	Weak transcription	Ovary	ovary
33	chr3:52085800-52089000	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr3:52085800-52089000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr3:52085800-52089000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:52086000-52087600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:52086000-52088400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
38	chr3:52086000-52089000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:52086000-52089000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr3:52086000-52089400	Enhancers	Fetal Heart	heart
41	chr3:52086200-52087600	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr3:52086200-52087600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr3:52086200-52087600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr3:52086200-52087600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr3:52086200-52087600	Flanking Active TSS	NH-A	brain
46	chr3:52086200-52087800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:52086200-52088000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
48	chr3:52086200-52088400	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:52086200-52088400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:52086200-52088400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin

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