Variant report

Variant	rs12050753
Chromosome Location	chr15:34531829-34531830
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	IRF1	chr15:34531627-34531832	K562	blood:	n/a	chr15:34531785-34531799 chr15:34531787-34531800 chr15:34531787-34531800 chr15:34531782-34531799 chr15:34531787-34531801 chr15:34531787-34531799 chr15:34531780-34531800 chr15:34531786-34531797 chr15:34531784-34531798 chr15:34531786-34531800
2	POLR2A	chr15:34531277-34532001	U87	brain:	n/a	n/a
3	FOS	chr15:34531583-34531943	Hela-S3	cervix:	n/a	chr15:34531696-34531707 chr15:34531751-34531759 chr15:34531749-34531760
4	POLR2A	chr15:34531393-34531917	U87	brain:	n/a	n/a
5	SP1	chr15:34531372-34532009	HCT-116	colon:	n/a	n/a
6	JUND	chr15:34530787-34532219	SK-N-SH	brain:	n/a	chr15:34531751-34531759
7	FOS	chr15:34531505-34532103	MCF10A-Er-Src	breast:	n/a	chr15:34531696-34531707 chr15:34531751-34531759 chr15:34531749-34531760
8	RAD21	chr15:34531608-34531935	Hela-S3	cervix:	n/a	n/a
9	FOS	chr15:34531542-34532043	MCF10A-Er-Src	breast:	n/a	chr15:34531696-34531707 chr15:34531751-34531759 chr15:34531749-34531760
10	SP1	chr15:34531278-34532061	HCT-116	colon:	n/a	n/a
11	FOSL1	chr15:34531318-34532137	HCT-116	colon:	n/a	chr15:34531751-34531759
12	STAT3	chr15:34531532-34532021	MCF10A-Er-Src	breast:	n/a	chr15:34531759-34531770 chr15:34531829-34531841 chr15:34531726-34531734
13	FOSL2	chr15:34531600-34532006	MCF-7	breast:	n/a	chr15:34531751-34531759
14	EP300	chr15:34531389-34532215	SK-N-SH	brain:	n/a	chr15:34531601-34531615 chr15:34531783-34531797
15	GATA3	chr15:34531429-34532270	SK-N-SH	brain:	n/a	n/a
16	STAT3	chr15:34531575-34532315	MCF10A-Er-Src	breast:	n/a	chr15:34531759-34531770 chr15:34531829-34531841 chr15:34531726-34531734
17	POLR2A	chr15:34531660-34531881	MCF10A-Er-Src	breast:	n/a	n/a
18	GATA3	chr15:34531407-34532279	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr15:34531653-34531886	HUVEC	blood vessel:	n/a	n/a
20	FOSL2	chr15:34531430-34531991	A549	lung:	n/a	chr15:34531751-34531759
21	POLR2A	chr15:34531460-34531917	U87	brain:	n/a	n/a
22	POLR2A	chr15:34531455-34532018	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr15:34531609-34531880	HCT-116	colon:	n/a	n/a
24	FOSL2	chr15:34531531-34531899	A549	lung:	n/a	chr15:34531751-34531759
25	POLR2A	chr15:34531460-34531994	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr15:34531271-34532001	U87	brain:	n/a	n/a
27	MYC	chr15:34531577-34532205	MCF10A-Er-Src	breast:	n/a	chr15:34531751-34531760
28	GATA3	chr15:34531623-34532094	MCF-7	breast:	n/a	n/a
29	TEAD4	chr15:34531382-34532046	SK-N-SH	brain:	n/a	n/a
30	JUND	chr15:34531369-34532149	SK-N-SH	brain:	n/a	chr15:34531751-34531759
31	STAT3	chr15:34531460-34532229	MCF10A-Er-Src	breast:	n/a	chr15:34531759-34531770 chr15:34531829-34531841 chr15:34531726-34531734 chr15:34531514-34531522
32	POLR2A	chr15:34531443-34532019	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr15:34531439-34532026	HUVEC	blood vessel:	n/a	n/a
34	NFIC	chr15:34531383-34532107	SK-N-SH	brain:	n/a	n/a
35	EP300	chr15:34531543-34531996	Hela-S3	cervix:	n/a	chr15:34531601-34531615 chr15:34531783-34531797
36	MAFK	chr15:34531276-34531973	IMR90	lung:	n/a	chr15:34531778-34531787
37	TCF12	chr15:34531406-34532191	SK-N-SH	brain:	n/a	n/a
38	FOS	chr15:34531514-34532018	MCF10A-Er-Src	breast:	n/a	chr15:34531696-34531707 chr15:34531751-34531759 chr15:34531749-34531760
39	JUN	chr15:34531511-34531966	HUVEC	blood vessel:	n/a	chr15:34531751-34531759
40	FOSL2	chr15:34531447-34532143	SK-N-SH	brain:	n/a	chr15:34531751-34531759
41	MYC	chr15:34531472-34532063	MCF10A-Er-Src	breast:	n/a	chr15:34531751-34531760
42	JUND	chr15:34531342-34532098	HCT-116	colon:	n/a	chr15:34531751-34531759
43	MAX	chr15:34531530-34531966	SK-N-SH	brain:	n/a	chr15:34531751-34531760
44	JUND	chr15:34531520-34531942	Hela-S3	cervix:	n/a	chr15:34531751-34531759
45	CBX3	chr15:34531079-34532089	HCT-116	colon:	n/a	n/a
46	FOSL1	chr15:34531412-34532052	HCT-116	colon:	n/a	chr15:34531751-34531759
47	JUND	chr15:34531341-34532173	SK-N-SH	brain:	n/a	chr15:34531751-34531759
48	FOS	chr15:34531508-34531994	MCF10A-Er-Src	breast:	n/a	chr15:34531696-34531707 chr15:34531751-34531759 chr15:34531749-34531760
49	JUND	chr15:34531385-34532091	HCT-116	colon:	n/a	chr15:34531751-34531759
50	JUND	chr15:34531574-34531909	H1-hESC	embryonic stem cell:	n/a	chr15:34531751-34531759

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	chr15:34500839..34504564-chr15:34529168..34532268,3	K562	blood:
5	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
ENSG00000134152	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10851964	0.82[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs1133154	0.84[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.81[YRI][hapmap];0.94[ASN][1000 genomes]
rs16958878	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs16958954	0.85[YRI][hapmap]
rs17236763	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17236777	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17236784	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17236798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17817806	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244040	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.98[ASN][1000 genomes]
rs2290940	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2290941	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2290942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705343	0.84[ASW][hapmap];0.90[GIH][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4238572	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4530104	0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs4577050	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs4780231	0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs4780232	0.85[ASN][1000 genomes]
rs4780233	0.84[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];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]
rs60604568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61549125	0.97[ASN][1000 genomes]
rs6495639	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6495646	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs7168761	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs7178002	0.82[CHD][hapmap]
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	1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs8036468	0.83[CHD][hapmap]
rs8040071	0.85[CHD][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap]

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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12050753	NOP10	cis	Esophagus Mucosa	GTEx
rs12050753	NOP10	cis	Muscle Skeletal	GTEx
rs12050753	NOLA3	cis	multi-tissue	Pritchard
rs12050753	TMEM85	cis	cerebellum	SCAN
rs12050753	NOP10	cis	Nerve Tibial	GTEx
rs12050753	NOP10	cis	Thyroid	GTEx
rs12050753	NOP10	cis	Heart Left Ventricle	GTEx
rs12050753	NOP10	cis	Artery Tibial	GTEx
rs12050753	SLC12A6	cis	Thyroid	GTEx
rs12050753	NOP10	cis	Esophagus Muscularis	GTEx
rs12050753	NOP10	cis	cerebellum	SCAN
rs12050753	NOP10	cis	parietal	SCAN

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	chr15:34523000-34532400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr15:34523000-34535800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:34523000-34545600	Weak transcription	Dnd41	blood
29	chr15:34523200-34532600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:34523800-34532400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:34524200-34533400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:34524200-34538200	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr15:34524200-34552400	Strong transcription	Primary B cells from cord blood	blood
34	chr15:34524400-34533400	Strong transcription	Adipose Nuclei	Adipose
35	chr15:34524400-34538000	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr15:34524600-34533400	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr15:34524800-34533200	Strong transcription	Brain Cingulate Gyrus	brain
38	chr15:34524800-34533600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr15:34524800-34533800	Strong transcription	Left Ventricle	heart
40	chr15:34524800-34553600	Strong transcription	Primary B cells from peripheral blood	blood
41	chr15:34525000-34532000	Strong transcription	Thymus	Thymus
42	chr15:34525000-34533400	Strong transcription	Fetal Thymus	thymus
43	chr15:34525200-34533200	Strong transcription	Fetal Lung	lung
44	chr15:34525200-34540400	Strong transcription	Primary T cells from cord blood	blood
45	chr15:34525400-34532000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr15:34525400-34533200	Strong transcription	Placenta	Placenta
47	chr15:34526200-34537000	Weak transcription	HepG2	liver
48	chr15:34526600-34533600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr15:34527000-34533200	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr15:34527200-34533200	Strong transcription	Primary hematopoietic stem cells	blood

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