Variant report

Variant	rs12905220
Chromosome Location	chr15:43757839-43757840
allele	C/G
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	chr15:43756265..43758113-chr15:43760726..43762348,2	K562	blood:
4	chr15:43756724..43759640-chr15:43771522..43773401,2	MCF-7	breast:
5	chr15:43756415..43758511-chr15:43785369..43787092,2	K562	blood:
6	15:43750262-43763629..15:44034348-44042259	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000167004	Chromatin interaction
ENSG00000067369	Chromatin interaction
ENSG00000205771	Chromatin interaction
ENSG00000166963	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];0.86[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]
rs12906017	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12906481	0.90[AMR][1000 genomes];1.00[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];0.92[EUR][1000 genomes]
rs12911569	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12911740	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[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];0.91[EUR][1000 genomes]
rs16957715	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[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];0.83[EUR][1000 genomes]
rs17780417	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17780920	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1814324	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2230451	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34002293	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34178146	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34181131	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34212866	0.90[AFR][1000 genomes];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	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34633582	0.83[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	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[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];0.86[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];0.97[EUR][1000 genomes]
rs35158584	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35160541	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35278805	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35326382	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35681736	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35903301	0.80[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	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36078097	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3862138	0.83[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	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55801120	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57728767	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57938858	0.86[EUR][1000 genomes]
rs60018990	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60367691	0.81[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	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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];0.89[EUR][1000 genomes]
rs62020616	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62021176	0.90[AMR][1000 genomes];0.89[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];1.00[EUR][1000 genomes]
rs71476435	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[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];0.83[EUR][1000 genomes]
rs7177146	1.00[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	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7181545	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7181634	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7181783	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7182292	0.81[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	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72709850	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72709879	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8027748	1.00[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12905220	ZSCAN29	cis	multi-tissue	Pritchard
rs12905220	LCMT2	cis	Esophagus Mucosa	GTEx
rs12905220	TGM7	cis	Esophagus Mucosa	GTEx
rs12905220	ZSCAN29	cis	Esophagus Muscularis	GTEx
rs12905220	TUBGCP4	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 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	chr15:43743600-43763400	Strong transcription	Fetal Muscle Trunk	muscle
10	chr15:43743800-43766800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:43743800-43770400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr15:43743800-43773400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:43744000-43760800	Strong transcription	Fetal Intestine Small	intestine
14	chr15:43744000-43762600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:43744000-43770600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:43744000-43770600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:43744000-43773400	Strong transcription	Fetal Muscle Leg	muscle
18	chr15:43744000-43773600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr15:43744000-43783000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr15:43744000-43784000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:43744200-43760400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:43746400-43782800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr15:43746600-43773000	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr15:43748000-43763400	Strong transcription	Dnd41	blood
25	chr15:43748800-43764800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr15:43749000-43760200	Weak transcription	Colonic Mucosa	Colon
27	chr15:43749000-43766800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr15:43749200-43759400	Weak transcription	Psoas Muscle	Psoas
29	chr15:43749200-43759400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr15:43749200-43765000	Weak transcription	Esophagus	oesophagus
31	chr15:43749200-43765000	Weak transcription	Gastric	stomach
32	chr15:43749200-43767200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr15:43749200-43769800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr15:43749200-43784600	Weak transcription	Stomach Mucosa	stomach
35	chr15:43749400-43758200	Weak transcription	Colon Smooth Muscle	Colon
36	chr15:43749400-43758800	Weak transcription	Brain Angular Gyrus	brain
37	chr15:43749400-43762600	Weak transcription	Brain Substantia Nigra	brain
38	chr15:43749400-43762800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr15:43749400-43764200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr15:43749400-43766600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr15:43749400-43766600	Weak transcription	HepG2	liver
42	chr15:43749400-43783800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr15:43749400-43784400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr15:43750400-43762400	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr15:43750600-43758400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr15:43750800-43765200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:43751000-43765600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:43751000-43766000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr15:43751200-43758000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr15:43751200-43760600	Weak transcription	K562	blood

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