Variant report

Variant	rs62021180
Chromosome Location	chr15:43712337-43712338
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:90286280..90287096-chr15:43711618..43712395,2	NB4	blood:

Variant related genes	Relation type
ENSG00000272931	Chromatin interaction
ENSG00000171492	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10518812	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12899865	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12900259	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12905220	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12906017	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12906481	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12907870	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12908460	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12911569	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12911740	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12913977	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12914122	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16957680	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16957715	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16957730	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17723479	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17780417	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17780920	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1814324	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2230451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34002293	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34178146	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34181131	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34212866	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34388946	0.81[EUR][1000 genomes]
rs34515241	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34591748	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34633582	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34657657	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34661349	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34697113	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34715468	0.85[AMR][1000 genomes]
rs34767197	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34860428	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34921640	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35158584	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35160541	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35278805	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35311230	0.83[AMR][1000 genomes]
rs35326382	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35681736	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35903301	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35958032	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35975365	0.86[EUR][1000 genomes]
rs35992154	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36078097	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3862138	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs514438	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55748552	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55801120	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57728767	0.85[EUR][1000 genomes]
rs60018990	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60367691	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62019432	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62019442	0.81[AMR][1000 genomes]
rs62020574	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62020575	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62020612	0.81[EUR][1000 genomes]
rs62021176	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66629206	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71476435	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7168220	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7173383	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7176923	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7177146	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7177892	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7180812	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7181545	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7181634	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7181783	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7182292	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7183708	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72707530	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72709850	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72709879	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8027748	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs62021180	LCMT2	cis	Esophagus Mucosa	GTEx
rs62021180	ZSCAN29	cis	multi-tissue	Pritchard
rs62021180	TUBGCP4	cis	Artery Tibial	GTEx
rs62021180	TGM7	cis	Esophagus Mucosa	GTEx
rs62021180	ZSCAN29	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43665000-43730000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:43668000-43717800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr15:43668200-43732800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:43675600-43744400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:43682800-43720800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr15:43682800-43727800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:43683400-43732200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:43685000-43720400	Strong transcription	Fetal Brain Female	brain
9	chr15:43686000-43717200	Strong transcription	Primary B cells from cord blood	blood
10	chr15:43686000-43717200	Strong transcription	Fetal Lung	lung
11	chr15:43686000-43720600	Strong transcription	Brain Germinal Matrix	brain
12	chr15:43686000-43727000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr15:43686400-43715400	Strong transcription	Fetal Intestine Large	intestine
14	chr15:43686600-43715800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:43686600-43720400	Strong transcription	Fetal Muscle Trunk	muscle
16	chr15:43686600-43720400	Strong transcription	Fetal Muscle Leg	muscle
17	chr15:43686600-43726000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr15:43686600-43733200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:43686600-43733800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr15:43686800-43717800	Strong transcription	Primary T cells from cord blood	blood
21	chr15:43686800-43725400	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr15:43686800-43725600	Strong transcription	Osteobl	bone
23	chr15:43686800-43733400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:43687000-43725400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:43687000-43732200	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr15:43687200-43733400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr15:43687600-43731600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:43689200-43737200	Weak transcription	Stomach Mucosa	stomach
29	chr15:43693400-43714200	Strong transcription	Hela-S3	cervix
30	chr15:43699200-43715400	Strong transcription	Stomach Smooth Muscle	stomach
31	chr15:43699200-43720400	Strong transcription	Fetal Stomach	stomach
32	chr15:43700000-43748400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr15:43702600-43712400	Weak transcription	Small Intestine	intestine
34	chr15:43703200-43739800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:43703600-43717800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:43703600-43731400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr15:43703800-43715400	Strong transcription	Ovary	ovary
38	chr15:43703800-43715800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:43703800-43724800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:43704000-43714400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:43704000-43718000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:43704000-43718000	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr15:43704200-43715800	Strong transcription	Fetal Intestine Small	intestine
44	chr15:43704200-43717800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:43704200-43727200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:43705400-43720800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:43705600-43712600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr15:43706200-43712400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr15:43706600-43712600	Weak transcription	HepG2	liver
50	chr15:43708400-43713600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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