Variant report

Variant	rs12568280
Chromosome Location	chr1:154122974-154122975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153962510..153964616-chr1:154122423..154124331,2	MCF-7	breast:
2	chr1:154121564..154123790-chr1:154128887..154131552,2	K562	blood:
3	chr1:154122896..154125457-chr1:154127729..154131254,3	MCF-7	breast:
4	chr1:154121866..154123799-chr1:154125577..154127582,4	K562	blood:

Variant related genes	Relation type
ENSG00000177954	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1051370	0.82[EUR][1000 genomes]
rs10797047	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4521985	0.82[EUR][1000 genomes]
rs60633748	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72696227	0.81[EUR][1000 genomes]
rs7535778	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription 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	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
7	nsv520398	chr1:154068196-154141908	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv1000153	chr1:154074249-154152417	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv872451	chr1:154101519-154139757	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12568280	UBAP2L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154112200-154138400	Weak transcription	Psoas Muscle	Psoas
2	chr1:154114600-154126800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:154119600-154127000	Weak transcription	Esophagus	oesophagus
4	chr1:154120200-154123600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:154121000-154125200	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr1:154121000-154127000	Weak transcription	Pancreas	Pancrea
7	chr1:154121400-154127000	Weak transcription	A549	lung
8	chr1:154121600-154123400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:154121600-154123800	Weak transcription	HUVEC	blood vessel
10	chr1:154121600-154125200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:154121600-154126200	Weak transcription	K562	blood
12	chr1:154121600-154126600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr1:154121800-154124000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:154121800-154126400	Weak transcription	Spleen	Spleen
15	chr1:154122000-154126200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:154122000-154126200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr1:154122000-154126800	Weak transcription	GM12878-XiMat	blood
18	chr1:154122200-154125800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:154122200-154126000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr1:154122200-154126400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:154122200-154126400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:154122200-154127000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:154122600-154126200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:154122600-154126400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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