Variant report

Variant	rs573778559
Chromosome Location	chr3:52088479-52088480
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52087181..52088866-chr3:52188475..52190351,2	K562	blood:
2	chr3:52028475..52031255-chr3:52087467..52089239,2	MCF-7	breast:
3	chr3:52087390..52089445-chr3:52228138..52231082,2	K562	blood:
4	chr3:52088419..52090155-chr3:52113932..52115849,2	K562	blood:
5	chr3:52026823..52031380-chr3:52087204..52091486,4	K562	blood:
6	chr3:51974895..51976742-chr3:52087202..52089493,2	K562	blood:
7	chr3:52087227..52088495-chr3:52178231..52179051,5	MCF-7	breast:
8	chr3:52015921..52019600-chr3:52088214..52092499,4	K562	blood:
9	chr3:52088066..52089919-chr3:52114349..52115931,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000243989	Chromatin interaction
ENSG00000164087	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000162244	Chromatin interaction
ENSG00000114767	Chromatin interaction
ENSG00000041880	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:18 , 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
17	nsv590281	chr3:52088204-52090396	Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
18	nsv590282	chr3:52088204-52097060	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr3:52082600-52088600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:52083200-52090200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:52084400-52088600	Genic enhancers	Placenta Amnion	Placenta Amnion
6	chr3:52084800-52088800	Transcr. at gene 5' and 3'	NHEK	skin
7	chr3:52084800-52090000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:52085000-52088600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:52085000-52089200	Enhancers	Primary B cells from peripheral blood	blood
10	chr3:52085000-52090200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:52085200-52088600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
12	chr3:52085200-52088800	Weak transcription	Small Intestine	intestine
13	chr3:52085400-52088600	Transcr. at gene 5' and 3'	Brain Angular Gyrus	brain
14	chr3:52085400-52088600	Transcr. at gene 5' and 3'	Brain Substantia Nigra	brain
15	chr3:52085400-52088800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr3:52085400-52088800	Enhancers	Stomach Mucosa	stomach
17	chr3:52085400-52089000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
18	chr3:52085600-52088800	Genic enhancers	Fetal Intestine Small	intestine
19	chr3:52085600-52088800	Transcr. at gene 5' and 3'	HMEC	breast
20	chr3:52085800-52088600	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
21	chr3:52085800-52088800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
22	chr3:52085800-52088800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:52085800-52088800	Weak transcription	Ovary	ovary
24	chr3:52085800-52089000	Flanking Active TSS	Primary T cells from cord blood	blood
25	chr3:52085800-52089000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr3:52085800-52089000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:52086000-52089000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:52086000-52089000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr3:52086000-52089400	Enhancers	Fetal Heart	heart
30	chr3:52086200-52088600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:52086200-52088600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:52086200-52088600	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:52086200-52088600	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
34	chr3:52086200-52089000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr3:52086200-52089000	Transcr. at gene 5' and 3'	Brain Inferior Temporal Lobe	brain
36	chr3:52086200-52090000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr3:52086400-52088600	Enhancers	Psoas Muscle	Psoas
38	chr3:52086400-52088600	Transcr. at gene 5' and 3'	Osteobl	bone
39	chr3:52086400-52089000	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
40	chr3:52086400-52090200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr3:52086600-52088600	Transcr. at gene 5' and 3'	Hela-S3	cervix
42	chr3:52086600-52089000	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
43	chr3:52086800-52088600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:52086800-52088600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:52086800-52088600	Genic enhancers	Brain Germinal Matrix	brain
46	chr3:52086800-52088800	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
47	chr3:52086800-52089000	Flanking Active TSS	GM12878-XiMat	blood
48	chr3:52086800-52089400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr3:52086800-52090800	Active TSS	Rectal Smooth Muscle	rectum
50	chr3:52087000-52088600	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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