Variant report

Variant	rs9309005
Chromosome Location	chr2:37548452-37548453
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	EP300	chr2:37548191-37553289	SK-N-SH	brain:	n/a	chr2:37553241-37553251 chr2:37551667-37551676 chr2:37551721-37551730 chr2:37552888-37552902 chr2:37552886-37552900 chr2:37548375-37548385 chr2:37552046-37552062 chr2:37551718-37551727 chr2:37551670-37551686 chr2:37551556-37551565 chr2:37549996-37550004 chr2:37551763-37551772 chr2:37552050-37552059 chr2:37552050-37552066 chr2:37551559-37551568 chr2:37551670-37551679 chr2:37551760-37551769 chr2:37551766-37551775
2	SPI1	chr2:37548426-37548708	GM12891	blood:	n/a	chr2:37548602-37548609 chr2:37548599-37548612
3	MXI1	chr2:37547850-37553154	SK-N-SH	brain:	n/a	n/a
4	SPI1	chr2:37548431-37548679	GM12891	blood:	n/a	chr2:37548602-37548609 chr2:37548599-37548612
5	SPI1	chr2:37548391-37548867	HL-60	blood:	n/a	chr2:37548602-37548609 chr2:37548599-37548612

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:37540781..37542934-chr2:37546496..37548956,2	MCF-7	breast:
2	chr2:37533235..37535380-chr2:37546761..37548910,2	MCF-7	breast:

Variant related genes	Relation type
PRKD3	TF binding region
ENSG00000232028	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10170761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1017158	1.00[AFR][1000 genomes]
rs1017159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10174658	1.00[ASN][1000 genomes]
rs10197287	1.00[ASN][1000 genomes]
rs10197856	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11124571	1.00[ASN][1000 genomes]
rs11124572	1.00[ASN][1000 genomes]
rs11883585	1.00[ASN][1000 genomes]
rs11886853	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890754	1.00[ASN][1000 genomes]
rs11892108	1.00[CHB][hapmap]
rs11896614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897904	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902292	1.00[ASN][1000 genomes]
rs13384958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392784	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13399143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13401288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13401291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409402	1.00[ASN][1000 genomes]
rs13414561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13422798	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13424642	1.00[ASN][1000 genomes]
rs13426217	1.00[ASN][1000 genomes]
rs13426239	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13426346	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13426780	1.00[ASN][1000 genomes]
rs13429945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17410072	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192945	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307472	1.00[CHB][hapmap]
rs2307483	1.00[CHB][hapmap]
rs2373114	1.00[CHB][hapmap]
rs28655786	1.00[ASN][1000 genomes]
rs28698067	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28710795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34149238	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4398251	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4648150	1.00[CHB][hapmap]
rs4648153	1.00[CHB][hapmap]
rs4648156	1.00[CHB][hapmap]
rs4648166	1.00[CHB][hapmap]
rs4648169	1.00[CHB][hapmap]
rs4648170	1.00[CHB][hapmap]
rs4648171	1.00[CHB][hapmap]
rs4648175	1.00[CHB][hapmap]
rs4648191	1.00[CHB][hapmap]
rs4648196	1.00[CHB][hapmap]
rs4648199	1.00[CHB][hapmap]
rs4648202	1.00[CHB][hapmap]
rs4648212	1.00[CHB][hapmap]
rs59712801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62133321	1.00[ASN][1000 genomes]
rs62133324	1.00[ASN][1000 genomes]
rs6711685	1.00[ASN][1000 genomes]
rs6715050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726768	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726921	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6727087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6727253	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730342	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6733861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748019	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6749793	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752475	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754376	1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs6754750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755577	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72792882	1.00[ASN][1000 genomes]
rs7556904	1.00[ASN][1000 genomes]
rs7556959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558593	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559558	1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs7573871	0.89[EUR][1000 genomes]
rs7582067	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590736	1.00[ASN][1000 genomes]
rs759460	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs759668	1.00[CHB][hapmap]
rs7598671	1.00[ASN][1000 genomes]
rs888098	1.00[ASN][1000 genomes]
rs888099	1.00[ASN][1000 genomes]
rs9309006	1.00[CEU][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]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430724	chr2:37546820-37628704	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9309005	PRKD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37484600-37550400	Weak transcription	Right Ventricle	heart
2	chr2:37509000-37550800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:37511000-37550800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:37519000-37549400	Weak transcription	HSMM	muscle
5	chr2:37520200-37549600	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:37520400-37549600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:37520400-37550400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr2:37530600-37550400	Weak transcription	Thymus	Thymus
9	chr2:37530800-37548600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:37530800-37549600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:37531000-37548600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:37533200-37550400	Weak transcription	Fetal Intestine Large	intestine
13	chr2:37533800-37549400	Weak transcription	Fetal Intestine Small	intestine
14	chr2:37534000-37550400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:37534400-37550400	Weak transcription	Lung	lung
16	chr2:37534400-37550600	Weak transcription	Left Ventricle	heart
17	chr2:37534800-37548800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:37535000-37548600	Weak transcription	HUVEC	blood vessel
19	chr2:37535000-37549400	Weak transcription	Hela-S3	cervix
20	chr2:37535400-37548600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:37537000-37550400	Weak transcription	HSMMtube	muscle
22	chr2:37538400-37549600	Weak transcription	Psoas Muscle	Psoas
23	chr2:37538600-37548600	Weak transcription	Liver	Liver
24	chr2:37539800-37548600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:37539800-37548800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:37540600-37548600	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:37542000-37550400	Weak transcription	Colonic Mucosa	Colon
28	chr2:37542400-37550800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:37542800-37549600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:37542800-37550800	Weak transcription	Gastric	stomach
31	chr2:37543000-37550400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr2:37543600-37548600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:37543600-37548800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:37543600-37548800	Weak transcription	Small Intestine	intestine
35	chr2:37543600-37549400	Weak transcription	Right Atrium	heart
36	chr2:37543600-37550400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:37543800-37550600	Weak transcription	Fetal Brain Male	brain
38	chr2:37545000-37548600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr2:37545600-37548600	Weak transcription	Fetal Thymus	thymus
40	chr2:37545800-37548800	Weak transcription	Aorta	Aorta
41	chr2:37545800-37549600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:37545800-37550400	Weak transcription	Ovary	ovary
43	chr2:37546000-37548600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr2:37546000-37548600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:37546000-37548600	Weak transcription	Fetal Heart	heart
46	chr2:37546000-37548800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr2:37546000-37548800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:37546000-37549200	Weak transcription	HMEC	breast
49	chr2:37546000-37549600	Weak transcription	Fetal Stomach	stomach
50	chr2:37546000-37550400	Weak transcription	H9 Cell Line	embryonic stem cell

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