Variant report

Variant	rs57494441
Chromosome Location	chr15:34520393-34520394
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:34497680..34504001-chr15:34514973..34521212,14	K562	blood:
2	chr15:34517046..34518726-chr15:34519236..34520864,2	K562	blood:
3	chr15:34515788..34518726-chr15:34518893..34520736,3	K562	blood:
4	chr15:34519148..34521644-chr15:34659451..34661317,2	K562	blood:

Variant related genes	Relation type
ENSG00000128463	Chromatin interaction
ENSG00000176454	Chromatin interaction
ENSG00000134152	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10851964	0.81[ASN][1000 genomes]
rs1133154	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12050753	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16958878	0.94[ASN][1000 genomes]
rs17236763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17236777	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17236784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236798	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17236819	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17817800	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17817806	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2244040	0.96[ASN][1000 genomes]
rs2290940	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2290941	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2290942	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2705343	0.81[AMR][1000 genomes]
rs4238572	0.91[ASN][1000 genomes]
rs4530104	0.89[ASN][1000 genomes]
rs4577050	0.81[ASN][1000 genomes]
rs4780231	0.86[ASN][1000 genomes]
rs4780232	0.86[ASN][1000 genomes]
rs4780233	0.93[ASN][1000 genomes]
rs4780234	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56761496	0.94[ASN][1000 genomes]
rs57626952	0.85[ASN][1000 genomes]
rs59023791	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs59091709	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs59209438	0.92[ASN][1000 genomes]
rs59712831	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60165224	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60604568	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61549125	0.94[ASN][1000 genomes]
rs6495639	0.90[ASN][1000 genomes]
rs6495646	0.97[ASN][1000 genomes]
rs73386033	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs73386037	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs73386038	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs73388003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73388020	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73388027	0.87[ASN][1000 genomes]
rs73388046	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73388049	0.87[ASN][1000 genomes]
rs8035954	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052804	chr15:34498529-34841447	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv542341	chr15:34498529-34841447	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1045173	chr15:34501055-34596995	Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs57494441	EMC4	cis	Esophagus Mucosa	GTEx
rs57494441	NOP10	cis	Artery Tibial	GTEx
rs57494441	NOP10	cis	Nerve Tibial	GTEx
rs57494441	NOP10	cis	Esophagus Mucosa	GTEx
rs57494441	NOP10	cis	Esophagus Muscularis	GTEx
rs57494441	SLC12A6	cis	Thyroid	GTEx
rs57494441	NOP10	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34517800-34531200	Weak transcription	Small Intestine	intestine
2	chr15:34518000-34520800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:34518000-34528000	Weak transcription	Aorta	Aorta
4	chr15:34518000-34532800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:34518000-34571800	Weak transcription	Stomach Mucosa	stomach
6	chr15:34518200-34520400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr15:34518200-34521600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr15:34518200-34521800	Weak transcription	Colonic Mucosa	Colon
9	chr15:34518200-34525600	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:34518200-34528800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr15:34518400-34520400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:34518400-34520400	Weak transcription	Lung	lung
13	chr15:34518400-34521400	Weak transcription	Pancreas	Pancrea
14	chr15:34518400-34522200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:34518400-34522400	Weak transcription	Right Ventricle	heart
16	chr15:34518400-34531000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr15:34518600-34520400	Weak transcription	HUVEC	blood vessel
18	chr15:34518800-34523200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:34518800-34524800	Strong transcription	Fetal Intestine Small	intestine
20	chr15:34518800-34524800	Strong transcription	Fetal Stomach	stomach
21	chr15:34518800-34529000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:34518800-34548200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr15:34519000-34522800	Strong transcription	Brain Substantia Nigra	brain
24	chr15:34519000-34523200	Strong transcription	Primary T cells from cord blood	blood
25	chr15:34519000-34523200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:34519000-34523200	Strong transcription	A549	lung
27	chr15:34519000-34523800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:34519000-34524000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:34519000-34552400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr15:34519200-34520800	Strong transcription	Ovary	ovary
31	chr15:34519200-34521000	Strong transcription	K562	blood
32	chr15:34519200-34522000	Weak transcription	Fetal Brain Male	brain
33	chr15:34519200-34523200	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:34519200-34523200	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr15:34519200-34523200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:34519200-34523200	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr15:34519200-34523200	Strong transcription	NH-A	brain
38	chr15:34519200-34523200	Strong transcription	NHEK	skin
39	chr15:34519200-34523400	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr15:34519200-34523400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:34519200-34523600	Strong transcription	HSMM	muscle
42	chr15:34519200-34523800	Strong transcription	Osteobl	bone
43	chr15:34519200-34530200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:34519200-34533200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:34519200-34534000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr15:34519200-34552200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr15:34519200-34553600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr15:34519400-34521000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr15:34519400-34521000	Strong transcription	NHDF-Ad	bronchial
50	chr15:34519400-34521000	Strong transcription	NHLF	lung

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