Variant report

Variant	rs3819892
Chromosome Location	chr2:37510416-37510417
allele	A/C
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	NFIC	chr2:37510195-37510936	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr2:37509752-37510940	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr2:37509832-37510872	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr2:37510197-37510789	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr2:37510178-37510740	HUVEC	blood vessel:	n/a	n/a
6	FOS	chr2:37510303-37510776	MCF10A-Er-Src	breast:	n/a	n/a
7	PBX3	chr2:37510221-37510865	SK-N-SH	brain:	n/a	n/a
8	MYC	chr2:37510380-37510665	MCF10A-Er-Src	breast:	n/a	n/a
9	TCF12	chr2:37510185-37510867	SK-N-SH	brain:	n/a	n/a
10	RAD21	chr2:37510358-37510629	IMR90	lung:	n/a	n/a
11	JUND	chr2:37510269-37510958	SK-N-SH	brain:	n/a	n/a
12	FOSL2	chr2:37510247-37510807	SK-N-SH	brain:	n/a	n/a
13	MEF2A	chr2:37509943-37510888	SK-N-SH	brain:	n/a	chr2:37510539-37510554 chr2:37510538-37510554 chr2:37510539-37510554 chr2:37510541-37510552
14	MYC	chr2:37510397-37510717	MCF10A-Er-Src	breast:	n/a	n/a
15	STAT3	chr2:37510351-37510720	MCF10A-Er-Src	breast:	n/a	chr2:37510447-37510459
16	FOS	chr2:37510384-37510744	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr2:37510402-37510769	MCF10A-Er-Src	breast:	n/a	n/a
18	RXRA	chr2:37510190-37510872	SK-N-SH	brain:	n/a	chr2:37510792-37510801
19	JUN	chr2:37510389-37510750	HUVEC	blood vessel:	n/a	n/a
20	MEF2A	chr2:37510143-37510956	SK-N-SH	brain:	n/a	chr2:37510539-37510554 chr2:37510538-37510554 chr2:37510539-37510554 chr2:37510541-37510552
21	CEBPB	chr2:37509909-37510701	IMR90	lung:	n/a	n/a
22	GATA3	chr2:37509698-37510898	SK-N-SH	brain:	n/a	chr2:37509810-37509817
23	FOSL2	chr2:37510259-37510887	SK-N-SH	brain:	n/a	n/a
24	FOS	chr2:37510303-37510782	MCF10A-Er-Src	breast:	n/a	n/a
25	MAFK	chr2:37510273-37510678	IMR90	lung:	n/a	n/a
26	EP300	chr2:37510161-37510855	SK-N-SH	brain:	n/a	chr2:37510824-37510838
27	FOS	chr2:37510369-37510768	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:37461002..37463569-chr2:37509247..37510932,2	K562	blood:

Variant related genes	Relation type
PRKD3	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10198835	0.93[CEU][hapmap]
rs11124576	1.00[ASW][hapmap];0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11124578	0.86[CEU][hapmap]
rs11689186	0.93[CEU][hapmap];0.81[CHD][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap];0.82[EUR][1000 genomes]
rs12622740	0.82[CHD][hapmap]
rs12712528	0.82[CHD][hapmap]
rs12712529	0.88[YRI][hapmap]
rs1477055	0.87[CEU][hapmap];0.87[TSI][hapmap]
rs17409947	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17481834	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2110963	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160394	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2268987	0.82[CEU][hapmap];0.87[TSI][hapmap]
rs2300881	0.87[CEU][hapmap]
rs2300884	0.87[CEU][hapmap];0.83[YRI][hapmap]
rs2300885	1.00[ASW][hapmap];0.93[CEU][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2300892	0.93[CEU][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2302650	0.93[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2302653	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2888463	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3770763	0.93[CEU][hapmap];0.85[JPT][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4670192	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4670689	0.88[YRI][hapmap]
rs55991517	0.94[EUR][1000 genomes]
rs56059107	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59262093	0.91[ASN][1000 genomes]
rs61208496	0.94[EUR][1000 genomes]
rs6726709	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72792821	0.94[EUR][1000 genomes]
rs72792835	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs876461	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9318	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3819892	QPCT	cis	parietal	SCAN
rs3819892	ATL2	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37460200-37528600	Weak transcription	Stomach Mucosa	stomach
2	chr2:37461200-37518800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:37467600-37530200	Weak transcription	Pancreas	Pancrea
4	chr2:37470400-37521600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:37470800-37521400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:37479400-37520600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr2:37482800-37528600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:37484200-37539000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr2:37484400-37511600	Weak transcription	Fetal Brain Male	brain
10	chr2:37484600-37550400	Weak transcription	Right Ventricle	heart
11	chr2:37487200-37528600	Weak transcription	Brain Substantia Nigra	brain
12	chr2:37487600-37521200	Weak transcription	Brain Angular Gyrus	brain
13	chr2:37490400-37510800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:37490600-37521000	Strong transcription	Dnd41	blood
15	chr2:37491000-37512400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:37492000-37510800	Strong transcription	Primary B cells from peripheral blood	blood
17	chr2:37492000-37511200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:37492800-37511200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:37495400-37510600	Strong transcription	Primary B cells from cord blood	blood
20	chr2:37499200-37520800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:37499200-37521400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr2:37499200-37522200	Weak transcription	Spleen	Spleen
23	chr2:37499400-37522800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:37499400-37528600	Weak transcription	Brain Anterior Caudate	brain
25	chr2:37499400-37540200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr2:37500200-37518600	Weak transcription	Fetal Stomach	stomach
27	chr2:37500200-37529800	Weak transcription	Fetal Intestine Small	intestine
28	chr2:37500200-37530200	Weak transcription	Gastric	stomach
29	chr2:37500400-37519200	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:37500400-37520400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr2:37500600-37530200	Weak transcription	Thymus	Thymus
32	chr2:37502200-37528200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:37502200-37528600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:37502400-37516200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:37502600-37513200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:37502600-37514600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:37502600-37517800	Weak transcription	Colonic Mucosa	Colon
38	chr2:37502600-37520000	Weak transcription	Fetal Brain Female	brain
39	chr2:37502600-37521600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:37502600-37524600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:37502600-37528600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:37502600-37532600	Weak transcription	Small Intestine	intestine
43	chr2:37502600-37533000	Weak transcription	Psoas Muscle	Psoas
44	chr2:37502600-37535800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr2:37502800-37514600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:37502800-37518400	Weak transcription	Ovary	ovary
47	chr2:37502800-37518600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr2:37502800-37528800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr2:37502800-37528800	Weak transcription	Brain Hippocampus Middle	brain
50	chr2:37502800-37533800	Weak transcription	Lung	lung

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