Variant report

Variant	rs17324884
Chromosome Location	chr4:119771477-119771478
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	chr4:119756043..119758170-chr4:119769333..119772030,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SYNPO2-1	chr4:119771440-119773194	NONHSAT098023
2	lnc-SYNPO2-1	chr4:119771465-119771743	NONHSAT098024

Variant related genes	Relation type
ENSG00000150961	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

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	0.92[CEU][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes]
rs11938970	0.92[CEU][hapmap]
rs17257039	0.83[CEU][hapmap]
rs17257945	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs17258050	0.83[CEU][hapmap]
rs17258106	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs17258830	1.00[CEU][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17258907	0.89[CEU][hapmap];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]
rs17323012	1.00[ASW][hapmap];0.92[CEU][hapmap]
rs17323034	1.00[ASW][hapmap];0.83[CEU][hapmap]
rs17323877	1.00[ASW][hapmap];0.83[CEU][hapmap];0.85[TSI][hapmap]
rs17324807	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17324821	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17324968	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[TSI][hapmap];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[ASW][hapmap];0.92[CEU][hapmap];0.85[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41535748	1.00[ASW][hapmap]
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]
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:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	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
3	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:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119764000-119771600	Weak transcription	HSMM	muscle
2	chr4:119764800-119771600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:119764800-119771800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:119770600-119772000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr4:119770600-119772000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr4:119770800-119771800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr4:119771000-119771600	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr4:119771000-119772800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr4:119771000-119773400	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr4:119771200-119771600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:119771200-119771600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:119771200-119771600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:119771200-119771600	Enhancers	HUVEC	blood vessel
14	chr4:119771200-119771600	Flanking Active TSS	NHDF-Ad	bronchial
15	chr4:119771200-119772400	Active TSS	Aorta	Aorta
16	chr4:119771200-119772400	Active TSS	Stomach Smooth Muscle	stomach
17	chr4:119771200-119772800	Flanking Active TSS	Dnd41	blood
18	chr4:119771200-119773400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr4:119771200-119773600	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr4:119771400-119771600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:119771400-119771600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr4:119771400-119771600	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr4:119771400-119771600	Enhancers	Primary B cells from cord blood	blood
24	chr4:119771400-119771600	Enhancers	Primary T cells from cord blood	blood
25	chr4:119771400-119771600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr4:119771400-119771600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:119771400-119771600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr4:119771400-119771600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:119771400-119771600	Enhancers	Muscle Satellite Cultured Cells	--
30	chr4:119771400-119771600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:119771400-119771600	Enhancers	Brain Angular Gyrus	brain
32	chr4:119771400-119771600	Enhancers	Fetal Intestine Large	intestine
33	chr4:119771400-119771600	Enhancers	Fetal Intestine Small	intestine
34	chr4:119771400-119771600	Enhancers	Fetal Lung	lung
35	chr4:119771400-119771600	Weak transcription	Psoas Muscle	Psoas
36	chr4:119771400-119771600	Enhancers	Stomach Mucosa	stomach
37	chr4:119771400-119771600	Enhancers	Thymus	Thymus
38	chr4:119771400-119771600	Enhancers	A549	lung
39	chr4:119771400-119771600	Flanking Active TSS	GM12878-XiMat	blood
40	chr4:119771400-119771600	Enhancers	Hela-S3	cervix
41	chr4:119771400-119771600	Active TSS	Monocytes-CD14+_RO01746	blood
42	chr4:119771400-119771800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr4:119771400-119771800	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr4:119771400-119771800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr4:119771400-119771800	Enhancers	Placenta Amnion	Placenta Amnion
46	chr4:119771400-119771800	Enhancers	Spleen	Spleen
47	chr4:119771400-119771800	Flanking Active TSS	NHEK	skin
48	chr4:119771400-119771800	Flanking Active TSS	Osteobl	bone
49	chr4:119771400-119772000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:119771400-119772000	Active TSS	Primary hematopoietic stem cells short term culture	blood

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