Variant report

Variant	rs72709850
Chromosome Location	chr15:43754684-43754685
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	15:43750262-43763629..15:43792489-43802874	K562	blood:
2	15:43750262-43763629..15:43802874-43806906	K562	blood:
3	chr15:43748496..43750673-chr15:43753283..43755737,2	K562	blood:
4	15:43750262-43763629..15:44034348-44042259	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000167004	Chromatin interaction
ENSG00000166963	Chromatin interaction
ENSG00000067369	Chromatin interaction
ENSG00000205771	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10518812	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12899865	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12900259	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12905220	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12906017	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12906481	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12907870	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12908460	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12911569	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12911740	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12913977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12914122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16957680	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16957715	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16957730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17723479	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17780417	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17780920	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1814324	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2230451	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34002293	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34178146	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34181131	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34212866	0.82[EUR][1000 genomes]
rs34388946	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34515241	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34591748	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34633582	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34657657	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34661349	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34697113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34767197	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34860428	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34921640	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35158584	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35160541	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35278805	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35311230	0.82[AFR][1000 genomes]
rs35326382	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35681736	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35903301	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35958032	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35992154	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36078097	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3862138	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs514438	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55748552	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55801120	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57728767	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57938858	0.86[EUR][1000 genomes]
rs60018990	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60367691	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62019432	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62020574	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62020575	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62020612	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62020616	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62021176	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62021180	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66629206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71476435	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7173383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7176923	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7177146	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7177892	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7180812	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7181545	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7181634	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7181783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7182292	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7183708	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72707530	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72709879	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8027748	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs72709850	TGM7	cis	Esophagus Mucosa	GTEx
rs72709850	LCMT2	cis	Esophagus Mucosa	GTEx
rs72709850	ZSCAN29	cis	Esophagus Muscularis	GTEx
rs72709850	TUBGCP4	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43726400-43769600	Weak transcription	Fetal Heart	heart
2	chr15:43730600-43765600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:43730600-43766800	Weak transcription	Small Intestine	intestine
4	chr15:43731200-43761400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:43734200-43780000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:43734200-43780200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:43739600-43761600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr15:43741600-43774800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:43743000-43755000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:43743000-43757000	Strong transcription	Fetal Stomach	stomach
11	chr15:43743600-43755200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:43743600-43763400	Strong transcription	Fetal Muscle Trunk	muscle
13	chr15:43743800-43766800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:43743800-43770400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:43743800-43773400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:43744000-43760800	Strong transcription	Fetal Intestine Small	intestine
17	chr15:43744000-43762600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:43744000-43770600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr15:43744000-43770600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:43744000-43773400	Strong transcription	Fetal Muscle Leg	muscle
21	chr15:43744000-43773600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr15:43744000-43783000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr15:43744000-43784000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:43744200-43760400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:43746200-43754800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:43746400-43755800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr15:43746400-43782800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr15:43746600-43754800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr15:43746600-43773000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr15:43747000-43755600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:43747600-43756000	Weak transcription	Right Atrium	heart
32	chr15:43747600-43756400	Strong transcription	Fetal Intestine Large	intestine
33	chr15:43747800-43757800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:43748000-43757000	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr15:43748000-43763400	Strong transcription	Dnd41	blood
36	chr15:43748800-43764800	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr15:43749000-43760200	Weak transcription	Colonic Mucosa	Colon
38	chr15:43749000-43766800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr15:43749200-43757200	Weak transcription	HMEC	breast
40	chr15:43749200-43759400	Weak transcription	Psoas Muscle	Psoas
41	chr15:43749200-43759400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr15:43749200-43765000	Weak transcription	Esophagus	oesophagus
43	chr15:43749200-43765000	Weak transcription	Gastric	stomach
44	chr15:43749200-43767200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr15:43749200-43769800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr15:43749200-43784600	Weak transcription	Stomach Mucosa	stomach
47	chr15:43749400-43755600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr15:43749400-43755800	Weak transcription	Primary B cells from cord blood	blood
49	chr15:43749400-43755800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr15:43749400-43756200	Weak transcription	Hela-S3	cervix

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