Variant report

Variant	rs12044616
Chromosome Location	chr1:154189417-154189418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:154188768-154189792	K562	blood:	n/a	n/a
2	POLR2A	chr1:154188773-154189509	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:154188655-154189428	K562	blood:	n/a	n/a
4	POLR2A	chr1:154188430-154195179	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr1:154188772-154191423	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:154189410-154189418	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr1:154188438-154189565	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154153141..154174161-chr1:154187746..154196033,47	MCF-7	breast:
2	chr1:154189134..154191972-chr1:154235587..154237500,3	MCF-7	breast:
3	chr1:154149113..154161877-chr1:154185436..154196776,24	K562	blood:

Variant related genes	Relation type
C1orf43	TF binding region
UBAP2L	TF binding region
ENSG00000143549	Chromatin interaction
ENSG00000215938	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10797058	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10797061	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908739	0.89[EUR][1000 genomes]
rs10908751	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265285	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1194580	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194582	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194599	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194600	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194602	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194603	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194604	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12063830	0.87[EUR][1000 genomes]
rs12095767	0.93[EUR][1000 genomes]
rs12354278	0.85[ASN][1000 genomes]
rs13796	0.85[ASN][1000 genomes]
rs2220390	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4072431	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4364874	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4393149	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4579747	0.87[EUR][1000 genomes]
rs4845609	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845610	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61807361	0.85[ASN][1000 genomes]
rs6680947	0.82[EUR][1000 genomes]
rs7516809	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7526644	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533952	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9803862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804045	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943097	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12044616	UBAP2L	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154172200-154190000	Weak transcription	Fetal Heart	heart
2	chr1:154177000-154191000	Strong transcription	Fetal Stomach	stomach
3	chr1:154177000-154192000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:154177200-154190200	Strong transcription	Primary T cells from cord blood	blood
5	chr1:154177400-154190400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:154177600-154191400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:154177800-154190400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:154177800-154190600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:154177800-154190600	Strong transcription	Fetal Intestine Small	intestine
10	chr1:154177800-154191000	Strong transcription	Fetal Muscle Leg	muscle
11	chr1:154177800-154191400	Strong transcription	Placenta	Placenta
12	chr1:154178000-154189800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:154178200-154191400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:154179400-154191000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:154180000-154191000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:154180200-154190800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:154183800-154191000	Weak transcription	Right Atrium	heart
18	chr1:154185200-154190000	Weak transcription	Esophagus	oesophagus
19	chr1:154185200-154192000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:154186200-154191000	Weak transcription	Fetal Brain Male	brain
21	chr1:154186400-154189800	Weak transcription	Hela-S3	cervix
22	chr1:154186400-154189800	Weak transcription	HUVEC	blood vessel
23	chr1:154186600-154189800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:154186600-154189800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:154186600-154190000	Weak transcription	Psoas Muscle	Psoas
26	chr1:154187000-154189800	Weak transcription	Adipose Nuclei	Adipose
27	chr1:154187000-154189800	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:154187000-154189800	Weak transcription	Pancreas	Pancrea
29	chr1:154187000-154189800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:154187000-154190000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:154187000-154190000	Weak transcription	Ovary	ovary
32	chr1:154187000-154190000	Weak transcription	Spleen	Spleen
33	chr1:154187000-154190400	Weak transcription	Fetal Brain Female	brain
34	chr1:154187000-154190400	Weak transcription	Small Intestine	intestine
35	chr1:154187000-154190400	Weak transcription	HSMMtube	muscle
36	chr1:154187000-154190400	Weak transcription	NHDF-Ad	bronchial
37	chr1:154187000-154190800	Weak transcription	Aorta	Aorta
38	chr1:154187000-154190800	Weak transcription	Right Ventricle	heart
39	chr1:154187000-154191400	Weak transcription	Colonic Mucosa	Colon
40	chr1:154187000-154191400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr1:154187000-154191800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:154187200-154189600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:154187200-154189600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr1:154187200-154189600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:154187200-154189600	Weak transcription	HSMM	muscle
46	chr1:154187200-154189600	Weak transcription	NH-A	brain
47	chr1:154187200-154189600	Weak transcription	Osteobl	bone
48	chr1:154187200-154189800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr1:154187200-154189800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:154187200-154189800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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