Variant report

Variant	rs59712831
Chromosome Location	chr15:34523445-34523446
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	chr15:34516443..34520692-chr15:34521035..34525736,7	MCF-7	breast:
2	chr15:34502586..34504102-chr15:34521539..34524042,2	K562	blood:

Variant related genes	Relation type
ENSG00000128463	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	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12050753	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16958878	0.94[ASN][1000 genomes]
rs17236763	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17236777	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17236784	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236798	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17236819	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17817800	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17817806	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2244040	0.96[ASN][1000 genomes]
rs2290940	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2290941	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2290942	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	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56761496	0.94[ASN][1000 genomes]
rs57494441	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57626952	0.85[ASN][1000 genomes]
rs59023791	0.96[ASN][1000 genomes]
rs59091709	0.96[ASN][1000 genomes]
rs59209438	0.92[ASN][1000 genomes]
rs60165224	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60604568	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	0.96[ASN][1000 genomes]
rs73386037	0.96[ASN][1000 genomes]
rs73386038	0.96[ASN][1000 genomes]
rs73388003	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73388020	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73388027	0.87[ASN][1000 genomes]
rs73388046	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
rs59712831	SLC12A6	cis	Thyroid	GTEx
rs59712831	NOP10	cis	Artery Tibial	GTEx
rs59712831	NOP10	cis	Esophagus Mucosa	GTEx
rs59712831	EMC4	cis	Esophagus Mucosa	GTEx
rs59712831	NOP10	cis	Esophagus Muscularis	GTEx
rs59712831	NOP10	cis	Thyroid	GTEx
rs59712831	NOP10	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 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	chr15:34518000-34528000	Weak transcription	Aorta	Aorta
3	chr15:34518000-34532800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:34518000-34571800	Weak transcription	Stomach Mucosa	stomach
5	chr15:34518200-34525600	Weak transcription	Colon Smooth Muscle	Colon
6	chr15:34518200-34528800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:34518400-34531000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr15:34518800-34524800	Strong transcription	Fetal Intestine Small	intestine
9	chr15:34518800-34524800	Strong transcription	Fetal Stomach	stomach
10	chr15:34518800-34529000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:34518800-34548200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:34519000-34523800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:34519000-34524000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:34519000-34552400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr15:34519200-34523600	Strong transcription	HSMM	muscle
16	chr15:34519200-34523800	Strong transcription	Osteobl	bone
17	chr15:34519200-34530200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:34519200-34533200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr15:34519200-34534000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr15:34519200-34552200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:34519200-34553600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:34519400-34523600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr15:34519400-34523600	Strong transcription	Adipose Nuclei	Adipose
24	chr15:34519400-34524000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr15:34519400-34530200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:34519400-34533200	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr15:34519400-34540800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:34519400-34552200	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr15:34519400-34552200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:34519600-34523600	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:34519600-34526600	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr15:34519600-34531800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr15:34519600-34533400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr15:34519600-34533400	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr15:34519600-34533600	Strong transcription	Fetal Muscle Trunk	muscle
36	chr15:34519600-34533600	Strong transcription	Fetal Muscle Leg	muscle
37	chr15:34519600-34538400	Strong transcription	Fetal Intestine Large	intestine
38	chr15:34519600-34544200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr15:34519600-34553600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr15:34519800-34531200	Strong transcription	GM12878-XiMat	blood
41	chr15:34519800-34533000	Strong transcription	Brain Anterior Caudate	brain
42	chr15:34519800-34540000	Strong transcription	Liver	Liver
43	chr15:34519800-34544800	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr15:34520000-34528000	Weak transcription	Fetal Kidney	kidney
45	chr15:34520000-34529600	Weak transcription	Fetal Heart	heart
46	chr15:34520000-34531400	Strong transcription	Fetal Brain Female	brain
47	chr15:34520200-34530200	Weak transcription	Psoas Muscle	Psoas
48	chr15:34520200-34555600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr15:34520600-34525600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr15:34520800-34526000	Weak transcription	Ovary	ovary

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