Variant report

Variant	rs2300888
Chromosome Location	chr2:37494336-37494337
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:37489176..37490982-chr2:37492972..37495639,2	K562	blood:
2	chr2:37425315..37427482-chr2:37493058..37494691,2	K562	blood:
3	chr2:37460312..37461934-chr2:37492568..37495549,2	K562	blood:
4	chr2:37486999..37491157-chr2:37494189..37497497,3	MCF-7	breast:
5	chr2:37493948..37499584-chr2:37500018..37504344,8	K562	blood:

Variant related genes	Relation type
ENSG00000115825	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10201396	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10204434	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10206380	0.81[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs10460527	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs11124570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11124573	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11124577	0.87[ASN][1000 genomes]
rs1160516	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11887618	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12469082	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12471267	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12476195	0.87[ASN][1000 genomes]
rs13390055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13412560	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs13421912	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13429526	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17020358	0.85[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2041838	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2041839	0.88[ASN][1000 genomes]
rs2075215	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs2075216	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs2192939	0.92[ASN][1000 genomes]
rs2216114	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239650	0.81[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap]
rs2251879	0.92[ASN][1000 genomes]
rs2268988	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2287091	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2287092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2300883	0.85[ASN][1000 genomes]
rs2300886	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2300887	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2300891	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2300894	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2300895	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2302649	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28524149	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3213746	0.80[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs3755192	0.85[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs3770761	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770767	1.00[ASN][1000 genomes]
rs3821144	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4610034	0.80[ASN][1000 genomes]
rs4629138	0.82[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4670682	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4670684	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4670685	0.81[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57861177	0.88[ASN][1000 genomes]
rs59559471	0.86[ASN][1000 genomes]
rs6709930	0.86[ASN][1000 genomes]
rs73927424	0.87[ASN][1000 genomes]
rs7593932	0.81[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs9309002	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952711	0.85[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs952712	0.85[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2300888	PRKD3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37460000-37495600	Weak transcription	Small Intestine	intestine
2	chr2:37460000-37501600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:37460200-37528600	Weak transcription	Stomach Mucosa	stomach
4	chr2:37460400-37498600	Weak transcription	Gastric	stomach
5	chr2:37460600-37498600	Weak transcription	Spleen	Spleen
6	chr2:37461200-37518800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:37463400-37509600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:37467600-37530200	Weak transcription	Pancreas	Pancrea
9	chr2:37470400-37498600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:37470400-37521600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:37470800-37521400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:37476800-37501400	Weak transcription	Esophagus	oesophagus
13	chr2:37477400-37502200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:37479400-37520600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr2:37479800-37501600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr2:37480600-37505000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:37481600-37500800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:37482600-37497800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr2:37482600-37501800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:37482800-37498600	Weak transcription	Lung	lung
21	chr2:37482800-37528600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:37483400-37498600	Weak transcription	HSMMtube	muscle
23	chr2:37483600-37498600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:37484000-37495400	Weak transcription	Thymus	Thymus
25	chr2:37484200-37501600	Weak transcription	K562	blood
26	chr2:37484200-37539000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr2:37484400-37511600	Weak transcription	Fetal Brain Male	brain
28	chr2:37484600-37498600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:37484600-37498600	Weak transcription	NHEK	skin
30	chr2:37484600-37500000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:37484600-37500400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:37484600-37501400	Weak transcription	Colonic Mucosa	Colon
33	chr2:37484600-37550400	Weak transcription	Right Ventricle	heart
34	chr2:37484800-37498600	Weak transcription	Aorta	Aorta
35	chr2:37485400-37494600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:37486200-37501600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:37486400-37495400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr2:37486400-37501200	Weak transcription	Psoas Muscle	Psoas
39	chr2:37486600-37495400	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:37486600-37495600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr2:37486600-37495600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr2:37486600-37497800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr2:37486600-37499000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:37486800-37495200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:37486800-37496000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:37486800-37496800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr2:37486800-37498400	Weak transcription	Ovary	ovary
48	chr2:37487200-37495600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:37487200-37528600	Weak transcription	Brain Substantia Nigra	brain
50	chr2:37487400-37495800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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