Variant report

Variant	rs8027748
Chromosome Location	chr15:43739820-43739821
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	15:43737704-43742060..15:43782117-43785993	H1-hESC	embryonic stem cell:	embryo
2	15:43737704-43742060..15:44080886-44089111	K562	blood:
3	15:43737704-43742060..15:43792489-43802874	K562	blood:
4	15:43737704-43742060..15:44034348-44042259	K562	blood:
5	15:43737704-43742060..15:43924442-43930824	GM12878	blood:
6	15:43737704-43742060..15:43802874-43806906	K562	blood:

Variant related genes	Relation type
ENSG00000166762	Chromatin interaction
ENSG00000206991	Chromatin interaction
ENSG00000140264	Chromatin interaction
ENSG00000067369	Chromatin interaction
ENSG00000167004	Chromatin interaction
ENSG00000242028	Chromatin interaction
ENSG00000205771	Chromatin interaction
ENSG00000166963	Chromatin interaction
ENSG00000221792	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10518812	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12899865	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12900259	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12905220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12906017	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12906481	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12907870	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12908460	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12911569	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12911740	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12913977	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12914122	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16957680	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16957715	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16957730	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17723479	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17780417	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17780920	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1814324	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2230451	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34002293	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34178146	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34181131	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34212866	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34388946	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34515241	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34591748	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34633582	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34657657	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34661349	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34697113	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34767197	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34860428	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34921640	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35158584	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35160541	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35278805	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35326382	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35681736	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35903301	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35958032	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35992154	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36078097	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3862138	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs514438	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55748552	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55801120	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57728767	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57938858	0.85[EUR][1000 genomes]
rs60018990	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60367691	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62019432	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62020574	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62020575	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62020612	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62020616	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62021176	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62021180	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66629206	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71476435	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7173383	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7176923	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7177146	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7177892	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7180812	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7181545	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7181634	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7181783	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7182292	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7183708	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72707530	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72709850	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72709879	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[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
rs8027748	ZSCAN29	cis	Esophagus Muscularis	GTEx
rs8027748	LCMT2	cis	Esophagus Mucosa	GTEx
rs8027748	ZSCAN29	cis	multi-tissue	Pritchard
rs8027748	TUBGCP4	cis	Artery Tibial	GTEx
rs8027748	TGM7	cis	Esophagus Mucosa	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43675600-43744400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:43700000-43748400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:43709400-43741600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:43713600-43750000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:43714000-43748200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:43715000-43747600	Weak transcription	Right Ventricle	heart
7	chr15:43715600-43748200	Weak transcription	Colonic Mucosa	Colon
8	chr15:43721600-43740200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:43722000-43740000	Strong transcription	Fetal Muscle Leg	muscle
10	chr15:43725000-43747800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:43725000-43748600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:43725000-43748800	Weak transcription	Esophagus	oesophagus
13	chr15:43726400-43748600	Weak transcription	Psoas Muscle	Psoas
14	chr15:43726400-43769600	Weak transcription	Fetal Heart	heart
15	chr15:43726800-43740000	Strong transcription	Fetal Stomach	stomach
16	chr15:43728200-43740000	Strong transcription	Fetal Intestine Large	intestine
17	chr15:43730600-43748000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:43730600-43748000	Weak transcription	Aorta	Aorta
19	chr15:43730600-43748000	Weak transcription	Fetal Brain Male	brain
20	chr15:43730600-43765600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr15:43730600-43766800	Weak transcription	Small Intestine	intestine
22	chr15:43731200-43761400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:43731800-43748000	Weak transcription	Spleen	Spleen
24	chr15:43731800-43752000	Weak transcription	Pancreas	Pancrea
25	chr15:43733200-43741000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:43733800-43747800	Weak transcription	Brain Angular Gyrus	brain
27	chr15:43733800-43748000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr15:43733800-43748400	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr15:43733800-43748600	Weak transcription	A549	lung
30	chr15:43734000-43748200	Weak transcription	Brain Substantia Nigra	brain
31	chr15:43734200-43748000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:43734200-43748000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr15:43734200-43748000	Weak transcription	HMEC	breast
34	chr15:43734200-43780000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:43734200-43780200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:43735400-43740200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr15:43735400-43743200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr15:43735600-43740000	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr15:43735600-43740000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr15:43735600-43740200	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr15:43735600-43740200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:43735800-43740000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:43735800-43740200	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr15:43735800-43740200	Strong transcription	Primary T cells from cord blood	blood
45	chr15:43736000-43744000	Weak transcription	Fetal Intestine Small	intestine
46	chr15:43736000-43748000	Weak transcription	K562	blood
47	chr15:43736200-43740000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:43736400-43740400	Strong transcription	Dnd41	blood
49	chr15:43736600-43740000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:43736800-43740000	Strong transcription	Rectal Mucosa Donor 31	rectum

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