Variant report

Variant	rs58629129
Chromosome Location	chr1:154910930-154910931
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:154908067-154911866	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:154910814-154910995	HepG2	liver:	n/a	n/a
3	HCFC1	chr1:154908381-154910940	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:154908163-154911416	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:154908478-154910936	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:154907338-154911035	SK-N-MC	brain:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154910185..154913057-chr1:155050643..155052609,2	MCF-7	breast:
2	chr1:154902125..154904691-chr1:154910364..154912646,2	K562	blood:
3	chr1:154907989..154910976-chr1:155021311..155023807,3	K562	blood:
4	chr1:154528898..154533098-chr1:154907799..154911445,7	MCF-7	breast:
5	chr1:154530603..154532117-chr1:154910041..154911705,2	K562	blood:
6	chr1:154907814..154911845-chr1:155021941..155025304,6	MCF-7	breast:
7	chr1:154910460..154912318-chr1:154915233..154917355,3	MCF-7	breast:
8	chr1:154908623..154911481-chr1:155056952..155059272,2	MCF-7	breast:
9	chr1:154910365..154912582-chr1:155016941..155018733,2	K562	blood:
10	chr1:154909403..154911372-chr1:155099659..155102635,3	MCF-7	breast:

No data

Variant related genes	Relation type
PMVK	TF binding region
ENSG00000169242	Chromatin interaction
ENSG00000143537	Chromatin interaction
ENSG00000143590	Chromatin interaction
ENSG00000232093	Chromatin interaction
ENSG00000160714	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10908447	0.85[AMR][1000 genomes]
rs11264276	0.85[AMR][1000 genomes]
rs11264281	0.82[AMR][1000 genomes]
rs11264291	1.00[ASN][1000 genomes]
rs12036859	0.82[AMR][1000 genomes]
rs12130132	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12144978	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12406380	0.80[ASN][1000 genomes]
rs2135219	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2335409	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4845399	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4845691	0.81[EUR][1000 genomes]
rs4845695	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6674853	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72702224	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7531728	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv872453	chr1:154904840-154995503	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
4	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58629129	PBXIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154909600-154911000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:154909800-154911000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr1:154910200-154911200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:154910200-154911400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:154910200-154911600	Flanking Active TSS	GM12878-XiMat	blood
6	chr1:154910200-154911800	Enhancers	Colonic Mucosa	Colon
7	chr1:154910200-154912400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:154910200-154912400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:154910200-154912600	Weak transcription	Gastric	stomach
10	chr1:154910200-154912600	Weak transcription	Spleen	Spleen
11	chr1:154910200-154912800	Weak transcription	Small Intestine	intestine
12	chr1:154910200-154913600	Weak transcription	Ovary	ovary
13	chr1:154910200-154913800	Weak transcription	Pancreas	Pancrea
14	chr1:154910200-154914200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:154910400-154911000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:154910400-154911200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:154910400-154911200	Enhancers	Fetal Intestine Small	intestine
18	chr1:154910400-154911400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:154910400-154911400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr1:154910400-154911600	Enhancers	Esophagus	oesophagus
21	chr1:154910400-154911800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:154910400-154911800	Enhancers	Left Ventricle	heart
23	chr1:154910400-154912000	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr1:154910400-154912400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr1:154910400-154912600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:154910400-154912600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:154910400-154912600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:154910400-154912600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:154910400-154912600	Weak transcription	Brain Substantia Nigra	brain
30	chr1:154910400-154912800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:154910400-154912800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:154910400-154913000	Enhancers	Fetal Intestine Large	intestine
33	chr1:154910400-154913000	Enhancers	Placenta	Placenta
34	chr1:154910400-154914800	Enhancers	Primary B cells from peripheral blood	blood
35	chr1:154910400-154914800	Enhancers	Fetal Thymus	thymus
36	chr1:154910400-154916600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:154910400-154916600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr1:154910400-154916800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:154910400-154917000	Enhancers	Primary hematopoietic stem cells	blood
40	chr1:154910400-154920000	Weak transcription	Aorta	Aorta
41	chr1:154910400-154923000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:154910400-154925000	Weak transcription	Psoas Muscle	Psoas
43	chr1:154910600-154911000	Enhancers	Right Ventricle	heart
44	chr1:154910600-154911000	Enhancers	HSMMtube	muscle
45	chr1:154910600-154911200	Enhancers	Primary B cells from cord blood	blood
46	chr1:154910600-154911200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr1:154910600-154911200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:154910600-154911400	Enhancers	Primary T cells from cord blood	blood
49	chr1:154910600-154911400	Enhancers	Brain Hippocampus Middle	brain
50	chr1:154910600-154911400	Enhancers	Rectal Smooth Muscle	rectum

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