Variant report

Variant	rs62019442
Chromosome Location	chr15:43649719-43649720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43646115..43650025-chr15:43654953..43659195,5	K562	blood:
2	chr15:43426164..43427738-chr15:43647862..43650071,2	K562	blood:
3	chr15:43476605..43479109-chr15:43648821..43650623,2	K562	blood:

Variant related genes	Relation type
ENSG00000137842	Chromatin interaction
ENSG00000261687	Chromatin interaction
ENSG00000166946	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10518812	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12908460	0.81[AMR][1000 genomes]
rs12911569	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16957680	0.81[AMR][1000 genomes]
rs16957715	0.81[AMR][1000 genomes]
rs17723479	0.81[EUR][1000 genomes]
rs17780417	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17780920	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1814324	0.81[EUR][1000 genomes]
rs2230451	0.81[AMR][1000 genomes]
rs34178146	0.82[EUR][1000 genomes]
rs34515241	0.82[EUR][1000 genomes]
rs34591748	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34657657	0.81[EUR][1000 genomes]
rs34767197	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34860428	0.81[AMR][1000 genomes]
rs35158584	0.81[AMR][1000 genomes]
rs35160541	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35278805	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35311230	0.81[AFR][1000 genomes]
rs35326382	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35681736	0.81[EUR][1000 genomes]
rs35992154	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs514438	0.80[EUR][1000 genomes]
rs55748552	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62019432	0.81[EUR][1000 genomes]
rs62021180	0.81[AMR][1000 genomes]
rs7176923	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7180812	0.81[AMR][1000 genomes]
rs7181634	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7183708	0.82[EUR][1000 genomes]
rs72707530	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS 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	47 gene(s)	inside rSNPs	diseases
2	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	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
4	nsv1512	chr15:43616834-43661646	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs62019442	LCMT2	cis	Esophagus Mucosa	GTEx
rs62019442	ZSCAN29	cis	Esophagus Muscularis	GTEx
rs62019442	TUBGCP4	cis	Artery Tibial	GTEx
rs62019442	TGM7	cis	Esophagus Mucosa	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43623200-43651000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr15:43623200-43651600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:43623200-43651600	Weak transcription	Pancreas	Pancrea
4	chr15:43623400-43650400	Weak transcription	Fetal Brain Male	brain
5	chr15:43623400-43651000	Weak transcription	Gastric	stomach
6	chr15:43623400-43651000	Weak transcription	Small Intestine	intestine
7	chr15:43623400-43653200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:43623600-43650400	Weak transcription	NH-A	brain
9	chr15:43623600-43650800	Weak transcription	HMEC	breast
10	chr15:43623600-43650800	Weak transcription	NHLF	lung
11	chr15:43623600-43651000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:43623600-43651000	Weak transcription	A549	lung
13	chr15:43623600-43653000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr15:43628400-43650400	Weak transcription	Primary B cells from cord blood	blood
15	chr15:43629200-43651000	Weak transcription	NHDF-Ad	bronchial
16	chr15:43630200-43650200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr15:43630400-43650400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:43630800-43650600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:43631600-43650400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr15:43631800-43651000	Weak transcription	Esophagus	oesophagus
21	chr15:43633200-43650600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr15:43633800-43650800	Weak transcription	Osteobl	bone
23	chr15:43634000-43651000	Weak transcription	Aorta	Aorta
24	chr15:43635400-43651000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:43639800-43650400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr15:43640400-43651000	Weak transcription	Fetal Kidney	kidney
27	chr15:43641200-43652800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr15:43641400-43650200	Weak transcription	Colon Smooth Muscle	Colon
29	chr15:43641400-43650600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:43641600-43649800	Weak transcription	Placenta	Placenta
31	chr15:43641600-43652800	Weak transcription	Hela-S3	cervix
32	chr15:43642200-43650800	Weak transcription	NHEK	skin
33	chr15:43643000-43651800	Weak transcription	Colonic Mucosa	Colon
34	chr15:43643400-43652800	Weak transcription	Right Ventricle	heart
35	chr15:43643600-43650400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr15:43643600-43650400	Weak transcription	Fetal Lung	lung
37	chr15:43643800-43650800	Weak transcription	Ovary	ovary
38	chr15:43644400-43650400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:43644400-43650800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:43644400-43650800	Weak transcription	Brain Hippocampus Middle	brain
41	chr15:43644400-43650800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr15:43644400-43650800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr15:43644400-43650800	Weak transcription	HepG2	liver
44	chr15:43644400-43651000	Weak transcription	Brain Angular Gyrus	brain
45	chr15:43644400-43651000	Weak transcription	Spleen	Spleen
46	chr15:43644400-43651800	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr15:43644600-43650200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr15:43644600-43650200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:43644600-43650400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr15:43644600-43650800	Weak transcription	Brain Substantia Nigra	brain

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