Variant report

Variant	rs17236777
Chromosome Location	chr15:34518211-34518212
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:34516767-34518325	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:34518004-34518309	HepG2	liver:	n/a	n/a
3	MXI1	chr15:34515886-34518224	SK-N-SH	brain:	n/a	n/a
4	ESRRA	chr15:34516281-34518261	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:34517851-34518424	GM12878	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:34391770..34396248-chr15:34515474..34518631,5	K562	blood:
2	chr15:34392855..34396101-chr15:34515904..34518783,5	MCF-7	breast:
3	chr15:34516456..34519073-chr15:34530589..34533176,2	MCF-7	breast:
4	chr15:34393239..34395470-chr15:34515986..34518807,4	MCF-7	breast:
5	chr15:34515223..34518649-chr15:34658701..34662221,4	K562	blood:
6	chr15:34516218..34520145-chr15:34531781..34533965,3	K562	blood:
7	chr15:34498121..34503791-chr15:34514506..34519551,14	K562	blood:
8	chr15:34515788..34518726-chr15:34518893..34520736,3	K562	blood:
9	chr15:34517046..34518726-chr15:34519236..34520864,2	K562	blood:
10	chr15:34516899..34519877-chr15:34627913..34631706,5	K562	blood:
11	chr15:34516899..34519877-chr15:34629611..34631706,2	K562	blood:
12	chr15:34497680..34504001-chr15:34514973..34521212,14	K562	blood:
13	chr15:34515594..34518445-chr15:34530011..34531536,2	K562	blood:
14	chr15:34516970..34518662-chr15:34536000..34538660,2	K562	blood:

No data

Variant related genes	Relation type
EMC4	TF binding region
ENSG00000128463	Chromatin interaction
ENSG00000134153	Chromatin interaction
ENSG00000176454	Chromatin interaction
ENSG00000140199	Chromatin interaction
ENSG00000182405	Chromatin interaction
ENSG00000134152	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10851964	0.81[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs1133154	0.86[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12050753	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]
rs16958878	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.81[YRI][hapmap];0.95[ASN][1000 genomes]
rs17236763	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17236798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17236819	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17817800	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17817806	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.97[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]
rs2244040	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs2290940	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2290941	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2290942	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2705343	0.90[GIH][hapmap];0.81[YRI][hapmap]
rs4238572	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.80[MEX][hapmap];0.92[ASN][1000 genomes]
rs4530104	0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs4577050	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs4780231	0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs4780232	0.86[ASN][1000 genomes]
rs4780233	0.84[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4780234	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56761496	0.95[ASN][1000 genomes]
rs57494441	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57626952	0.86[ASN][1000 genomes]
rs59023791	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs59091709	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs59209438	0.93[ASN][1000 genomes]
rs59712831	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60165224	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60604568	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61549125	0.95[ASN][1000 genomes]
rs6495639	0.94[JPT][hapmap];0.87[YRI][hapmap];0.89[ASN][1000 genomes]
rs6495646	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs7168761	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs7178002	0.82[CHD][hapmap]
rs73386033	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs73386037	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs73386038	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs73388003	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73388020	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73388027	0.88[ASN][1000 genomes]
rs73388046	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73388049	0.88[ASN][1000 genomes]
rs8035954	1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs8036468	0.83[CHD][hapmap]
rs8040071	0.85[CHD][hapmap];0.84[JPT][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs17236777	NOP10	cis	Esophagus Muscularis	GTEx
rs17236777	NOLA3	cis	multi-tissue	Pritchard
rs17236777	NOP10	cis	Thyroid	GTEx
rs17236777	NOP10	cis	cerebellum	SCAN
rs17236777	NOP10	cis	parietal	SCAN
rs17236777	NOP10	cis	Artery Tibial	GTEx
rs17236777	NOP10	cis	Esophagus Mucosa	GTEx
rs17236777	NOP10	cis	Nerve Tibial	GTEx
rs17236777	SLC12A6	cis	Thyroid	GTEx
rs17236777	TMEM85	cis	cerebellum	SCAN
rs17236777	EMC4	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34516000-34518400	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr15:34516000-34518400	Active TSS	Fetal Intestine Small	intestine
3	chr15:34516000-34518400	Active TSS	A549	lung
4	chr15:34516000-34518400	Active TSS	K562	blood
5	chr15:34516200-34518400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:34516200-34518400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr15:34516200-34518400	Active TSS	HSMM	muscle
8	chr15:34516200-34518600	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr15:34516400-34518400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr15:34516400-34518400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:34517400-34518400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr15:34517400-34518400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:34517400-34518400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:34517400-34518400	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr15:34517400-34518400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr15:34517600-34518400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr15:34517600-34518400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr15:34517600-34518400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:34517600-34518400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:34517600-34518400	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr15:34517600-34518400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr15:34517600-34518400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr15:34517600-34518400	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr15:34517600-34518400	Flanking Active TSS	Dnd41	blood
25	chr15:34517600-34518400	Flanking Active TSS	GM12878-XiMat	blood
26	chr15:34517600-34518600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:34517800-34518400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
28	chr15:34517800-34518400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:34517800-34518400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr15:34517800-34518400	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr15:34517800-34518400	Flanking Active TSS	Brain Germinal Matrix	brain
32	chr15:34517800-34518400	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr15:34517800-34518400	Flanking Active TSS	Hela-S3	cervix
34	chr15:34517800-34518400	Flanking Active TSS	HMEC	breast
35	chr15:34517800-34518400	Flanking Active TSS	NHEK	skin
36	chr15:34517800-34518400	Flanking Active TSS	Osteobl	bone
37	chr15:34517800-34531200	Weak transcription	Small Intestine	intestine
38	chr15:34518000-34518400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr15:34518000-34518400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:34518000-34518400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr15:34518000-34518400	Enhancers	Primary B cells from peripheral blood	blood
42	chr15:34518000-34518400	Enhancers	Primary T cells fromperipheralblood	blood
43	chr15:34518000-34518400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr15:34518000-34518400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:34518000-34518400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:34518000-34518400	Enhancers	Brain Substantia Nigra	brain
47	chr15:34518000-34518400	Enhancers	Placenta	Placenta
48	chr15:34518000-34518400	Enhancers	Fetal Stomach	stomach
49	chr15:34518000-34518400	Enhancers	Fetal Thymus	thymus
50	chr15:34518000-34518400	Enhancers	Left Ventricle	heart

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