Variant report

Variant	rs55748552
Chromosome Location	chr15:43651626-43651627
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43645456..43647561-chr15:43650775..43652983,2	K562	blood:
2	chr15:43621538..43624484-chr15:43650651..43653663,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LCMT2-1	chr15:43650376-43652236	NONHSAT042065

Variant related genes	Relation type
ENSG00000168806	Chromatin interaction
ENSG00000168803	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10518812	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12899865	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12900259	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12905220	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12906017	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12906481	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12907870	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12908460	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12911569	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12911740	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12913977	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12914122	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16957680	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16957715	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16957730	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17723479	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17780417	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17780920	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1814324	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2230451	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34002293	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34178146	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34181131	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34212866	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34515241	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34591748	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34633582	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34657657	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34661349	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34697113	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34715468	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs34767197	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34860428	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34921640	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35158584	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35160541	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35278805	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35311230	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35326382	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35681736	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35903301	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35958032	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35975365	0.93[EUR][1000 genomes]
rs35992154	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36078097	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs514438	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55801120	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57728767	0.85[AFR][1000 genomes]
rs60018990	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62019432	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62019442	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62020574	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62020575	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62021176	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62021180	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66629206	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71476435	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7168220	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7173383	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7176923	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7177146	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7177892	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7180812	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7181545	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7181634	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7181783	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7182292	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7183708	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72707530	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72709850	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72709879	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8027748	0.95[AMR][1000 genomes];0.84[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs55748552	TGM7	cis	Esophagus Mucosa	GTEx
rs55748552	ZSCAN29	cis	multi-tissue	Pritchard
rs55748552	TUBGCP4	cis	Artery Tibial	GTEx
rs55748552	ZSCAN29	cis	Esophagus Muscularis	GTEx
rs55748552	LCMT2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43623400-43653200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:43623600-43653000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:43641200-43652800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:43641600-43652800	Weak transcription	Hela-S3	cervix
5	chr15:43643000-43651800	Weak transcription	Colonic Mucosa	Colon
6	chr15:43643400-43652800	Weak transcription	Right Ventricle	heart
7	chr15:43644400-43651800	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr15:43646800-43656200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:43647200-43652800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr15:43647200-43652800	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:43648800-43652400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:43648800-43653000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:43649200-43655400	ZNF genes & repeats	Fetal Intestine Large	intestine
14	chr15:43649200-43658600	ZNF genes & repeats	Liver	Liver
15	chr15:43649400-43652200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:43649600-43652800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:43649800-43653200	Strong transcription	Placenta	Placenta
18	chr15:43649800-43654000	ZNF genes & repeats	Fetal Intestine Small	intestine
19	chr15:43649800-43660000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
20	chr15:43649800-43660200	ZNF genes & repeats	Fetal Muscle Leg	muscle
21	chr15:43650000-43652800	Strong transcription	Brain Germinal Matrix	brain
22	chr15:43650200-43652200	ZNF genes & repeats	Colon Smooth Muscle	Colon
23	chr15:43650200-43652800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:43650200-43652800	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr15:43650200-43653000	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr15:43650200-43655000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:43650200-43656800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
28	chr15:43650200-43657000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
29	chr15:43650200-43657400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr15:43650200-43657600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
31	chr15:43650200-43657800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr15:43650200-43657800	ZNF genes & repeats	Adipose Nuclei	Adipose
33	chr15:43650200-43658600	ZNF genes & repeats	GM12878-XiMat	blood
34	chr15:43650200-43659800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:43650200-43660400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
36	chr15:43650200-43661600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:43650400-43652000	Strong transcription	Fetal Brain Male	brain
38	chr15:43650400-43652200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
39	chr15:43650400-43652400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr15:43650400-43652600	Strong transcription	Brain Anterior Caudate	brain
41	chr15:43650400-43652800	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr15:43650400-43652800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr15:43650400-43652800	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr15:43650400-43653200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:43650400-43653600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr15:43650400-43654800	ZNF genes & repeats	HSMM	muscle
47	chr15:43650400-43655200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
48	chr15:43650400-43656200	ZNF genes & repeats	NH-A	brain
49	chr15:43650400-43656600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
50	chr15:43650400-43657000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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