Variant report

Variant	rs56227053
Chromosome Location	chr4:119772460-119772461
allele	C/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
3	lnc-SYNPO2-1	chr4:119772409-119772685	NONHSAT098024

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]
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]
rs56302493	1.00[AFR][1000 genomes];1.00[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:45 , 50 per page) page: 1

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	chr4:119771200-119772800	Flanking Active TSS	Dnd41	blood
4	chr4:119771200-119773400	Active TSS	H9 Cell Line	embryonic stem cell
5	chr4:119771200-119773600	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr4:119771400-119772600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:119771400-119772600	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr4:119771400-119772600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr4:119771400-119772600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:119771400-119772600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:119771400-119772600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr4:119771400-119772600	Active TSS	Right Atrium	heart
13	chr4:119771400-119772600	Active TSS	HMEC	breast
14	chr4:119771400-119772800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:119771400-119773400	Active TSS	H1 Cell Line	embryonic stem cell
16	chr4:119771600-119772600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:119771600-119772800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:119771600-119773000	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr4:119771600-119773800	Active TSS	GM12878-XiMat	blood
20	chr4:119771800-119772600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:119771800-119773600	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr4:119772000-119772600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr4:119772000-119772800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:119772000-119773000	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr4:119772000-119773200	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr4:119772200-119772600	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr4:119772200-119772600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr4:119772200-119773000	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr4:119772200-119774400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:119772400-119772600	Enhancers	Primary B cells from peripheral blood	blood
31	chr4:119772400-119772600	Active TSS	Primary T cells from cord blood	blood
32	chr4:119772400-119772600	Enhancers	Primary T cells fromperipheralblood	blood
33	chr4:119772400-119772600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr4:119772400-119772600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr4:119772400-119772600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:119772400-119772600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr4:119772400-119772800	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr4:119772400-119772800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr4:119772400-119773400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr4:119772400-119773400	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr4:119772400-119773400	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr4:119772400-119773400	Enhancers	Liver	Liver
43	chr4:119772400-119774000	Weak transcription	HUVEC	blood vessel
44	chr4:119772400-119779200	Weak transcription	Ovary	ovary
45	chr4:119772400-119788200	Weak transcription	NHDF-Ad	bronchial

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