Variant report

Variant	rs11264290
Chromosome Location	chr1:154912300-154912301
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:154912102-154915919	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:154530535..154533107-chr1:154911658..154914567,2	MCF-7	breast:
2	chr1:154910185..154913057-chr1:155050643..155052609,2	MCF-7	breast:
3	chr1:154902125..154904691-chr1:154910364..154912646,2	K562	blood:
4	chr1:154910460..154912318-chr1:154915233..154917355,3	MCF-7	breast:
5	chr1:154878831..154879518-chr1:154911649..154912316,2	MCF-7	breast:
6	chr1:154910365..154912582-chr1:155016941..155018733,2	K562	blood:

No data

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

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1007170	0.97[ASN][1000 genomes]
rs10796934	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10796935	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10908444	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10908445	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10908446	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10908447	0.91[ASN][1000 genomes]
rs10908448	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1109815	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264280	0.81[ASN][1000 genomes]
rs11264281	0.91[ASN][1000 genomes]
rs11264282	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11264283	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11264284	0.93[ASN][1000 genomes]
rs11264291	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12036859	0.91[ASN][1000 genomes]
rs12069356	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12095061	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130132	0.97[ASN][1000 genomes]
rs12406380	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1580943	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1976559	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1977879	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2061690	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2102423	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2135219	0.91[ASN][1000 genomes]
rs2174507	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2335407	0.83[ASN][1000 genomes]
rs2335408	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335409	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738026	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4240874	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4240875	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4339857	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4578216	0.86[ASN][1000 genomes]
rs4845398	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4845400	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845677	0.80[ASN][1000 genomes]
rs4845678	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4845679	0.91[ASN][1000 genomes]
rs4845680	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4845681	0.87[ASN][1000 genomes]
rs4845682	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845683	0.93[ASN][1000 genomes]
rs4845685	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4845687	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845688	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845689	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845690	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845691	0.97[ASN][1000 genomes]
rs4845692	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4845693	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845694	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845695	0.98[ASN][1000 genomes]
rs4845696	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656435	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6656494	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6669791	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6674853	0.97[ASN][1000 genomes]
rs6683557	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6686873	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699043	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705094	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72702224	1.00[ASN][1000 genomes]
rs7528532	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7544528	0.83[ASN][1000 genomes]
rs7553195	0.80[ASN][1000 genomes]
rs869506	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs877343	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883718	0.82[AMR][1000 genomes]
rs906593	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9793588	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][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
rs11264290	PBXIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154910200-154912400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:154910200-154912400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:154910200-154912600	Weak transcription	Gastric	stomach
4	chr1:154910200-154912600	Weak transcription	Spleen	Spleen
5	chr1:154910200-154912800	Weak transcription	Small Intestine	intestine
6	chr1:154910200-154913600	Weak transcription	Ovary	ovary
7	chr1:154910200-154913800	Weak transcription	Pancreas	Pancrea
8	chr1:154910200-154914200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:154910400-154912400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:154910400-154912600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:154910400-154912600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:154910400-154912600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:154910400-154912600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:154910400-154912600	Weak transcription	Brain Substantia Nigra	brain
15	chr1:154910400-154912800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:154910400-154912800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:154910400-154913000	Enhancers	Fetal Intestine Large	intestine
18	chr1:154910400-154913000	Enhancers	Placenta	Placenta
19	chr1:154910400-154914800	Enhancers	Primary B cells from peripheral blood	blood
20	chr1:154910400-154914800	Enhancers	Fetal Thymus	thymus
21	chr1:154910400-154916600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:154910400-154916600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr1:154910400-154916800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:154910400-154917000	Enhancers	Primary hematopoietic stem cells	blood
25	chr1:154910400-154920000	Weak transcription	Aorta	Aorta
26	chr1:154910400-154923000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:154910400-154925000	Weak transcription	Psoas Muscle	Psoas
28	chr1:154910600-154912600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:154910600-154912600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:154910600-154912600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:154910600-154912600	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr1:154910600-154912600	Weak transcription	Fetal Brain Female	brain
33	chr1:154910600-154912600	Weak transcription	Fetal Lung	lung
34	chr1:154910600-154912600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:154910600-154912800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr1:154910600-154912800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr1:154910600-154913000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:154910600-154913600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:154910600-154913800	Weak transcription	Fetal Stomach	stomach
40	chr1:154910600-154914000	Weak transcription	A549	lung
41	chr1:154910600-154914400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:154910600-154914800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:154910600-154915000	Enhancers	Primary T cells fromperipheralblood	blood
44	chr1:154910600-154915000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:154910600-154915400	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr1:154910600-154916800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:154910600-154927200	Weak transcription	Fetal Kidney	kidney
48	chr1:154910800-154912400	Weak transcription	Fetal Muscle Leg	muscle
49	chr1:154910800-154912600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr1:154910800-154912600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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