Variant report

Variant	rs56302493
Chromosome Location	chr4:119772382-119772383
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:119758473..119760374-chr4:119771765..119773281,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SYNPO2-2	chr4:119771867-119772488	XLOC_003665
2	lnc-SYNPO2-1	chr4:119771440-119773194	NONHSAT098023

Variant related genes	Relation type
ENSG00000150961	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10001115	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10018977	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10019311	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10025640	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11098451	0.93[EUR][1000 genomes]
rs17257945	0.88[EUR][1000 genomes]
rs17258106	0.88[EUR][1000 genomes]
rs17258830	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17258907	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17259173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17259257	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17259284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17324807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17324821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17324884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17324968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17325017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17325129	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17325192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28595532	0.93[EUR][1000 genomes]
rs28600971	0.93[EUR][1000 genomes]
rs28627331	0.88[EUR][1000 genomes]
rs28797314	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28837152	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41455648	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55633605	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55640619	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55649377	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55668908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55671478	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55704595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55726697	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55744948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55758547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55794497	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55806110	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55823625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55869953	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55901549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55913633	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55985953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56027489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56042726	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56046449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56046676	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56055826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56104443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56117870	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56124677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56144225	1.00[AFR][1000 genomes]
rs56150431	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56162974	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56212415	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56227053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56252481	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56264833	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56283736	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56291421	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56302600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56303276	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56309519	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56322132	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56331118	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56342843	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56359736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56364904	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56388366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56389935	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs56762141	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6818519	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73842253	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3376985	chr4:119757182-119774736	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119771000-119772800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr4:119771000-119773400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr4:119771200-119772400	Active TSS	Aorta	Aorta
4	chr4:119771200-119772400	Active TSS	Stomach Smooth Muscle	stomach
5	chr4:119771200-119772800	Flanking Active TSS	Dnd41	blood
6	chr4:119771200-119773400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr4:119771200-119773600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr4:119771400-119772400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:119771400-119772400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:119771400-119772400	Flanking Active TSS	Primary B cells from peripheral blood	blood
11	chr4:119771400-119772400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr4:119771400-119772400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr4:119771400-119772400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
14	chr4:119771400-119772400	Active TSS	Adipose Nuclei	Adipose
15	chr4:119771400-119772400	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr4:119771400-119772400	Active TSS	Ovary	ovary
17	chr4:119771400-119772400	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr4:119771400-119772400	Active TSS	NHLF	lung
19	chr4:119771400-119772600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:119771400-119772600	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr4:119771400-119772600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr4:119771400-119772600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:119771400-119772600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:119771400-119772600	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr4:119771400-119772600	Active TSS	Right Atrium	heart
26	chr4:119771400-119772600	Active TSS	HMEC	breast
27	chr4:119771400-119772800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:119771400-119773400	Active TSS	H1 Cell Line	embryonic stem cell
29	chr4:119771600-119772400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr4:119771600-119772400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:119771600-119772400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr4:119771600-119772400	Active TSS	Fetal Intestine Large	intestine
33	chr4:119771600-119772400	Active TSS	Fetal Intestine Small	intestine
34	chr4:119771600-119772400	Active TSS	Fetal Lung	lung
35	chr4:119771600-119772400	Flanking Active TSS	Thymus	Thymus
36	chr4:119771600-119772400	Flanking Active TSS	HUVEC	blood vessel
37	chr4:119771600-119772600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr4:119771600-119772800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr4:119771600-119773000	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr4:119771600-119773800	Active TSS	GM12878-XiMat	blood
41	chr4:119771800-119772400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:119771800-119772400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
43	chr4:119771800-119772400	Active TSS	Placenta	Placenta
44	chr4:119771800-119772400	Active TSS	Psoas Muscle	Psoas
45	chr4:119771800-119772600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr4:119771800-119773600	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr4:119772000-119772400	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr4:119772000-119772400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr4:119772000-119772400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr4:119772000-119772400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links