Variant report

Variant	rs17709867
Chromosome Location	chr15:42800767-42800768
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr15:42800467-42800854	K562	blood:	n/a	n/a
2	CHD2	chr15:42800649-42800844	K562	blood:	n/a	n/a
3	POLR2A	chr15:42798220-42800951	K562	blood:	n/a	n/a
4	CTCF	chr15:42800640-42800790	AoAF	blood vessel:	n/a	n/a
5	POLR2A	chr15:42800739-42800814	HepG2	liver:	n/a	n/a
6	POLR2A	chr15:42800496-42800990	K562	blood:	n/a	n/a
7	PBX3	chr15:42800505-42800963	SK-N-SH	brain:	n/a	n/a
8	MAZ	chr15:42800486-42800833	K562	blood:	n/a	n/a
9	TBL1XR1	chr15:42800378-42800830	K562	blood:	n/a	n/a
10	ZNF384	chr15:42800318-42800800	K562	blood:	n/a	n/a
11	JUND	chr15:42800424-42800947	K562	blood:	n/a	n/a
12	POLR2A	chr15:42800749-42800781	HUVEC	blood vessel:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42799730..42801498-chr15:42803071..42806879,3	K562	blood:
2	chr15:42799625..42802317-chr15:42839494..42842081,2	K562	blood:

No data

Variant related genes	Relation type
SNAP23	TF binding region
ENSG00000180979	Chromatin interaction
ENSG00000137814	Chromatin interaction
ENSG00000092531	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10454692	0.87[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1048571	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11070375	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11630625	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11630681	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11633112	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11635041	0.87[EUR][1000 genomes]
rs11635076	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11635889	0.94[CEU][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11636209	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11636577	0.80[TSI][hapmap]
rs12438021	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12439003	1.00[LWK][hapmap]
rs12439377	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12440118	0.87[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs12440506	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12910538	0.82[AMR][1000 genomes]
rs17709596	0.85[EUR][1000 genomes]
rs17766258	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17767264	1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17767270	1.00[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2595938	0.81[EUR][1000 genomes]
rs41315252	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56069741	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56172155	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62019280	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62019282	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62019285	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62019287	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62019288	0.81[EUR][1000 genomes]
rs62019294	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62019312	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62019315	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62019320	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62019322	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62022313	0.80[EUR][1000 genomes]
rs62022315	0.80[EUR][1000 genomes]
rs62022316	0.85[EUR][1000 genomes]
rs62022318	0.84[EUR][1000 genomes]
rs7182376	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72711767	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8039240	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8042618	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17709867	CEP27	Cis_1M	lymphoblastoid	RTeQTL
rs17709867	SNAP23	cis	parietal	SCAN
rs17709867	TUBGCP4	cis	cerebellum	SCAN
rs17709867	INO80	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42788400-42808000	Weak transcription	Esophagus	oesophagus
2	chr15:42788600-42805600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr15:42788600-42806600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:42788600-42807200	Weak transcription	Fetal Kidney	kidney
5	chr15:42788800-42805200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr15:42788800-42805400	Weak transcription	Brain Germinal Matrix	brain
7	chr15:42789000-42803400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:42789000-42805400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr15:42789000-42806400	Weak transcription	Thymus	Thymus
10	chr15:42789200-42802400	Weak transcription	Fetal Brain Female	brain
11	chr15:42789200-42804400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr15:42789200-42805800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:42789200-42806600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:42790400-42802600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr15:42790600-42805200	Weak transcription	Dnd41	blood
16	chr15:42790600-42806600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr15:42790600-42807200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr15:42790800-42805000	Weak transcription	Fetal Thymus	thymus
19	chr15:42790800-42809800	Weak transcription	Spleen	Spleen
20	chr15:42790800-42810000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr15:42790800-42821400	Weak transcription	Right Ventricle	heart
22	chr15:42791200-42803800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr15:42791200-42809800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:42792200-42802400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr15:42792200-42803000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr15:42792200-42805800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:42792400-42802800	Weak transcription	NH-A	brain
28	chr15:42792400-42803400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr15:42792400-42804000	Weak transcription	NHEK	skin
30	chr15:42792400-42805400	Weak transcription	Fetal Muscle Leg	muscle
31	chr15:42792400-42806600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:42792400-42807400	Weak transcription	HMEC	breast
33	chr15:42792600-42802800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:42792600-42805600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr15:42793000-42809800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:42793000-42835600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr15:42793200-42802400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:42793200-42803400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr15:42793200-42803600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr15:42793400-42802600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:42793600-42805400	Weak transcription	Liver	Liver
42	chr15:42793600-42807400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr15:42793800-42801800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:42793800-42802400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr15:42793800-42806400	Weak transcription	Pancreas	Pancrea
46	chr15:42793800-42837200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr15:42795200-42802400	Weak transcription	Hela-S3	cervix
48	chr15:42796400-42801000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr15:42796400-42802400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr15:42796600-42803800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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