Variant report

Variant	rs60604568
Chromosome Location	chr15:34532726-34532727
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:34532694-34534153	A549	lung:	n/a	chr15:34533758-34533779

No.	Distal block	Cell Line	Cell type
1	chr15:34531119..34534573-chr15:34628473..34631118,3	MCF-7	breast:
2	chr15:34526514..34531481-chr15:34531605..34533762,5	K562	blood:
3	chr15:34516218..34520145-chr15:34531781..34533965,3	K562	blood:
4	chr15:34516456..34519073-chr15:34530589..34533176,2	MCF-7	breast:

Variant related genes	Relation type
SLC12A6	TF binding region
ENSG00000128463	Chromatin interaction
ENSG00000140199	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10851964	0.83[ASN][1000 genomes]
rs1133154	0.94[ASN][1000 genomes]
rs12050753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16958878	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17236763	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17236777	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17236784	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17236798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17817800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17817806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244040	0.98[ASN][1000 genomes]
rs2290940	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2290941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2290942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705343	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4238572	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4530104	0.86[ASN][1000 genomes]
rs4577050	0.83[ASN][1000 genomes]
rs4780231	0.85[ASN][1000 genomes]
rs4780232	0.85[ASN][1000 genomes]
rs4780233	0.94[ASN][1000 genomes]
rs4780234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56761496	0.97[ASN][1000 genomes]
rs57494441	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57626952	0.85[ASN][1000 genomes]
rs59023791	0.95[ASN][1000 genomes]
rs59091709	0.94[ASN][1000 genomes]
rs59209438	0.95[ASN][1000 genomes]
rs59712831	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60165224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61549125	0.97[ASN][1000 genomes]
rs6495639	0.91[ASN][1000 genomes]
rs6495646	0.99[ASN][1000 genomes]
rs73386033	0.95[ASN][1000 genomes]
rs73386037	0.95[ASN][1000 genomes]
rs73386038	0.95[ASN][1000 genomes]
rs73388003	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73388020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73388027	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73388046	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73388049	0.90[ASN][1000 genomes]
rs8035954	0.87[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs60604568	NOP10	cis	Esophagus Muscularis	GTEx
rs60604568	NOP10	cis	Nerve Tibial	GTEx
rs60604568	NOP10	cis	Artery Tibial	GTEx
rs60604568	NOP10	cis	Esophagus Mucosa	GTEx
rs60604568	NOP10	cis	Heart Left Ventricle	GTEx
rs60604568	SLC12A6	cis	Thyroid	GTEx
rs60604568	NOP10	cis	Thyroid	GTEx
rs60604568	NOP10	cis	Muscle Skeletal	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34518000-34532800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:34518000-34571800	Weak transcription	Stomach Mucosa	stomach
3	chr15:34518800-34548200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:34519000-34552400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr15:34519200-34533200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr15:34519200-34534000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr15:34519200-34552200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:34519200-34553600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr15:34519400-34533200	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr15:34519400-34540800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:34519400-34552200	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr15:34519400-34552200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:34519600-34533400	Strong transcription	Duodenum Mucosa	Duodenum
14	chr15:34519600-34533400	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr15:34519600-34533600	Strong transcription	Fetal Muscle Trunk	muscle
16	chr15:34519600-34533600	Strong transcription	Fetal Muscle Leg	muscle
17	chr15:34519600-34538400	Strong transcription	Fetal Intestine Large	intestine
18	chr15:34519600-34544200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr15:34519600-34553600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr15:34519800-34533000	Strong transcription	Brain Anterior Caudate	brain
21	chr15:34519800-34540000	Strong transcription	Liver	Liver
22	chr15:34519800-34544800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr15:34520200-34555600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr15:34521000-34532800	Weak transcription	K562	blood
25	chr15:34521000-34547800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:34523000-34535800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:34523000-34545600	Weak transcription	Dnd41	blood
28	chr15:34524200-34533400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr15:34524200-34538200	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr15:34524200-34552400	Strong transcription	Primary B cells from cord blood	blood
31	chr15:34524400-34533400	Strong transcription	Adipose Nuclei	Adipose
32	chr15:34524400-34538000	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr15:34524600-34533400	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr15:34524800-34533200	Strong transcription	Brain Cingulate Gyrus	brain
35	chr15:34524800-34533600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:34524800-34533800	Strong transcription	Left Ventricle	heart
37	chr15:34524800-34553600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr15:34525000-34533400	Strong transcription	Fetal Thymus	thymus
39	chr15:34525200-34533200	Strong transcription	Fetal Lung	lung
40	chr15:34525200-34540400	Strong transcription	Primary T cells from cord blood	blood
41	chr15:34525400-34533200	Strong transcription	Placenta	Placenta
42	chr15:34526200-34537000	Weak transcription	HepG2	liver
43	chr15:34526600-34533600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr15:34527000-34533200	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr15:34527200-34533200	Strong transcription	Primary hematopoietic stem cells	blood
46	chr15:34527800-34533200	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr15:34528400-34535600	Weak transcription	Fetal Brain Male	brain
48	chr15:34528400-34546400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr15:34528400-34547400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr15:34528600-34532800	Weak transcription	H1 Cell Line	embryonic stem cell

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