Variant report

Variant	rs267307
Chromosome Location	chr5:114598204-114598205
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:1)
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	chr2:10262275..10263092-chr5:114598074..114598869,2	HCT-116	colon:
2	chr5:114598026..114600265-chr5:114601043..114603821,2	K562	blood:
3	chr5:114596880..114599090-chr5:114631128..114633570,2	MCF-7	breast:
4	chr5:114596551..114598881-chr5:114630526..114633575,4	MCF-7	breast:
5	chr5:114509837..114512434-chr5:114598149..114599681,2	MCF-7	breast:
6	chr12:92539214..92539929-chr5:114598092..114598989,2	Hela-S3	cervix:
7	chr5:114598157..114598878-chr6:159240087..159240668,2	HCT-116	colon:
8	chr5:114588379..114591127-chr5:114596921..114598565,2	MCF-7	breast:
9	chr5:114593990..114598856-chr5:114605325..114609897,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AP3S1-15	chr5:114598202-114599145	ENSG00000271797.1

No data

Variant related genes	Relation type
ENSG00000171848	Chromatin interaction
ENSG00000164219	Chromatin interaction
ENSG00000092820	Chromatin interaction
ENSG00000243304	Chromatin interaction
ENSG00000133639	Chromatin interaction
ENSG00000152503	Chromatin interaction
ENSG00000245904	Chromatin interaction
ENSG00000164221	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs117060	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs155414	0.91[CHB][hapmap]
rs166459	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs169088	0.92[CHB][hapmap]
rs17137563	0.90[LWK][hapmap]
rs185566	0.81[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes]
rs190561	0.83[ASN][1000 genomes]
rs2053697	0.85[CHB][hapmap];0.89[CHD][hapmap]
rs2112360	0.85[AMR][1000 genomes]
rs2112361	0.85[AMR][1000 genomes]
rs2124396	0.89[AMR][1000 genomes]
rs2545430	0.85[AMR][1000 genomes]
rs265412	0.93[CHD][hapmap];0.83[JPT][hapmap]
rs265419	0.92[CHB][hapmap]
rs265420	0.92[CHB][hapmap]
rs265421	0.92[CHB][hapmap];0.92[CHD][hapmap]
rs265425	0.89[CHB][hapmap];0.92[CHD][hapmap]
rs265430	0.92[CHB][hapmap];0.96[CHD][hapmap]
rs265435	0.83[CHB][hapmap]
rs265436	0.92[CHB][hapmap]
rs265438	0.81[ASN][1000 genomes]
rs265439	0.92[CHB][hapmap]
rs265442	0.92[CHB][hapmap];0.96[CHD][hapmap]
rs267286	0.81[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.89[MEX][hapmap];0.87[AMR][1000 genomes]
rs267287	0.81[CEU][hapmap];0.83[CHB][hapmap];0.87[AMR][1000 genomes]
rs267288	0.81[CEU][hapmap];0.83[CHB][hapmap];0.87[AMR][1000 genomes]
rs267290	0.89[AMR][1000 genomes]
rs267292	0.85[AMR][1000 genomes]
rs267295	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs267297	0.89[CHD][hapmap]
rs267298	0.92[CHB][hapmap];0.93[CHD][hapmap]
rs267299	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs267300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs267301	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs267302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs267303	0.92[CHB][hapmap];0.96[CHD][hapmap]
rs267304	1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[ASN][1000 genomes]
rs267306	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3100784	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830454	chr5:114453864-114607159	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs267307	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114596800-114599200	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr5:114597000-114598600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr5:114597000-114598800	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr5:114597000-114598800	Active TSS	Right Ventricle	heart
5	chr5:114597000-114599000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:114597000-114599000	Active TSS	Psoas Muscle	Psoas
7	chr5:114597000-114599200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:114597200-114598800	Active TSS	Fetal Intestine Large	intestine
9	chr5:114597200-114599000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:114597200-114599000	Active TSS	Aorta	Aorta
11	chr5:114597200-114599000	Active TSS	K562	blood
12	chr5:114597200-114599200	Active TSS	NHDF-Ad	bronchial
13	chr5:114597200-114599400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr5:114597400-114598400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr5:114597400-114598600	Active TSS	Colonic Mucosa	Colon
16	chr5:114597400-114598600	Active TSS	GM12878-XiMat	blood
17	chr5:114597400-114598800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:114597400-114598800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:114597400-114598800	Active TSS	Esophagus	oesophagus
20	chr5:114597400-114598800	Active TSS	Placenta Amnion	Placenta Amnion
21	chr5:114597400-114599000	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr5:114597400-114599000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:114597400-114599000	Active TSS	Fetal Intestine Small	intestine
24	chr5:114597400-114599000	Active TSS	Fetal Muscle Trunk	muscle
25	chr5:114597400-114599000	Active TSS	Left Ventricle	heart
26	chr5:114597400-114599200	Active TSS	H1 Cell Line	embryonic stem cell
27	chr5:114597400-114599200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:114597400-114599200	Active TSS	Ovary	ovary
29	chr5:114597400-114599200	Active TSS	Stomach Smooth Muscle	stomach
30	chr5:114597400-114599200	Active TSS	A549	lung
31	chr5:114597600-114598600	Active TSS	Muscle Satellite Cultured Cells	--
32	chr5:114597600-114598600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:114597600-114598600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:114597600-114598600	Active TSS	HMEC	breast
35	chr5:114597600-114598800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr5:114597600-114598800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:114597600-114598800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:114597600-114598800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr5:114597600-114598800	Bivalent/Poised TSS	HepG2	liver
40	chr5:114597600-114598800	Active TSS	HSMMtube	muscle
41	chr5:114597600-114598800	Active TSS	NHLF	lung
42	chr5:114597600-114599000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr5:114597600-114599000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr5:114597600-114599000	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr5:114597600-114599000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr5:114597600-114599000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:114597600-114599000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr5:114597600-114599000	Active TSS	Fetal Stomach	stomach
49	chr5:114597600-114599000	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr5:114597600-114599000	Active TSS	HSMM	muscle

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