Variant report

Variant	rs12239415
Chromosome Location	chr1:225635483-225635484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225633322..225636010-chr1:226185928..226188018,2	K562	blood:
2	chr1:225615892..225618526-chr1:225635437..225638461,3	K562	blood:
3	chr1:225633065..225638606-chr1:225639136..225643843,7	MCF-7	breast:
4	chr1:225632782..225636036-chr1:225646050..225649453,3	K562	blood:

Variant related genes	Relation type
ENSG00000143751	Chromatin interaction
ENSG00000143815	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10449249	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10915829	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11377355	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12022013	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12026034	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12031651	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12037289	0.82[ASN][1000 genomes]
rs12042273	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12405879	0.83[ASN][1000 genomes]
rs12405904	0.83[ASN][1000 genomes]
rs1340866	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1340870	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1340871	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1340872	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16845000	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2184778	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2185531	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28620013	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3766931	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4129816	0.81[ASN][1000 genomes]
rs55751087	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56169721	0.82[ASN][1000 genomes]
rs58269599	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59912270	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61333083	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6674621	0.82[ASN][1000 genomes]
rs6681559	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6684314	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6684956	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6694938	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74146931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74146994	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74149835	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs74149844	0.82[ASN][1000 genomes]
rs7543444	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv34905	chr1:225631404-225676582	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12239415	LBR	cis	Artery Tibial	GTEx
rs12239415	LBR	cis	Esophagus Muscularis	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225625400-225636000	Enhancers	Colon Smooth Muscle	Colon
2	chr1:225626000-225636200	Enhancers	Fetal Intestine Large	intestine
3	chr1:225629200-225636400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr1:225629400-225635600	Enhancers	Primary hematopoietic stem cells	blood
5	chr1:225629400-225635600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:225630200-225636400	Enhancers	Fetal Intestine Small	intestine
7	chr1:225630800-225636600	Enhancers	Fetal Muscle Leg	muscle
8	chr1:225632200-225635800	Enhancers	Fetal Stomach	stomach
9	chr1:225632200-225637800	Enhancers	Stomach Mucosa	stomach
10	chr1:225632400-225635800	Enhancers	Placenta	Placenta
11	chr1:225632400-225636200	Enhancers	Fetal Lung	lung
12	chr1:225632600-225635800	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr1:225632800-225636600	Enhancers	Esophagus	oesophagus
14	chr1:225633000-225636000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:225633000-225636400	Enhancers	Right Atrium	heart
16	chr1:225633000-225640200	Enhancers	Fetal Thymus	thymus
17	chr1:225633200-225635600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:225633200-225635600	Enhancers	Small Intestine	intestine
19	chr1:225633200-225635800	Enhancers	Primary T cells fromperipheralblood	blood
20	chr1:225633200-225635800	Enhancers	Lung	lung
21	chr1:225633200-225635800	Enhancers	Right Ventricle	heart
22	chr1:225633200-225636000	Enhancers	Fetal Kidney	kidney
23	chr1:225633400-225635600	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr1:225633400-225635600	Enhancers	Gastric	stomach
25	chr1:225633400-225635800	Enhancers	Fetal Heart	heart
26	chr1:225633400-225636200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr1:225633400-225636600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr1:225633400-225637800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr1:225633600-225635600	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr1:225633600-225635600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:225633600-225637200	Enhancers	Hela-S3	cervix
32	chr1:225633600-225642000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:225633800-225635600	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr1:225633800-225635600	Weak transcription	A549	lung
35	chr1:225633800-225635800	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr1:225633800-225636000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:225633800-225636200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
38	chr1:225633800-225637800	Enhancers	Colonic Mucosa	Colon
39	chr1:225633800-225638400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:225634000-225635600	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr1:225634000-225635800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:225634000-225635800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:225634000-225635800	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr1:225634000-225636200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:225634000-225636400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:225634200-225636400	Weak transcription	HMEC	breast
47	chr1:225634200-225638000	Enhancers	Duodenum Mucosa	Duodenum
48	chr1:225634200-225642000	Weak transcription	K562	blood
49	chr1:225634400-225635600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:225634400-225636400	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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