Variant report

Variant	rs1160516
Chromosome Location	chr2:37506228-37506229
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10201396	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10204434	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10206380	0.85[JPT][hapmap]
rs10460527	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11124570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11124573	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11124577	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11887618	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12469082	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12471267	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476195	0.88[ASN][1000 genomes]
rs13390055	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13412560	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13421912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429526	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs17020344	0.82[EUR][1000 genomes]
rs17020358	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2041838	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2041839	0.89[ASN][1000 genomes]
rs2075215	0.95[JPT][hapmap]
rs2075216	0.95[JPT][hapmap]
rs2192939	0.92[ASN][1000 genomes]
rs2216114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239650	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2241163	0.80[ASN][1000 genomes]
rs2251879	0.92[ASN][1000 genomes]
rs2268988	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2287091	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2300883	0.86[ASN][1000 genomes]
rs2300886	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2300887	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2300888	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]
rs2300891	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2300894	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2300895	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2302649	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs28524149	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3213746	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs3755192	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs3770761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770767	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3821144	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4610034	0.81[ASN][1000 genomes]
rs4629138	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4670682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4670684	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4670685	1.00[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57861177	0.88[ASN][1000 genomes]
rs59559471	0.87[ASN][1000 genomes]
rs6709930	0.86[ASN][1000 genomes]
rs73927424	0.88[ASN][1000 genomes]
rs7593932	0.84[JPT][hapmap]
rs9309002	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9309003	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]
rs9309006	0.82[CEU][hapmap]
rs952711	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs952712	0.81[CHB][hapmap];0.95[JPT][hapmap]

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	nsv828953	chr2:37505113-37506297	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1160516	PRKD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 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	chr2:37463400-37509600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:37467600-37530200	Weak transcription	Pancreas	Pancrea
5	chr2:37470400-37521600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:37470800-37521400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:37479400-37520600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:37482800-37528600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:37484200-37539000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr2:37484400-37511600	Weak transcription	Fetal Brain Male	brain
11	chr2:37484600-37550400	Weak transcription	Right Ventricle	heart
12	chr2:37487200-37528600	Weak transcription	Brain Substantia Nigra	brain
13	chr2:37487600-37521200	Weak transcription	Brain Angular Gyrus	brain
14	chr2:37490400-37507000	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:37490400-37510800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:37490600-37521000	Strong transcription	Dnd41	blood
17	chr2:37491000-37512400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:37491200-37510200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:37491200-37510200	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr2:37491800-37509400	Strong transcription	Osteobl	bone
21	chr2:37492000-37507000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:37492000-37509600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:37492000-37510800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr2:37492000-37511200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:37492400-37510000	Weak transcription	Fetal Heart	heart
26	chr2:37492800-37511200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:37493200-37508000	Weak transcription	NHLF	lung
28	chr2:37494000-37510200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:37495400-37509800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:37495400-37510600	Strong transcription	Primary B cells from cord blood	blood
31	chr2:37499000-37510400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:37499200-37520800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr2:37499200-37521400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:37499200-37522200	Weak transcription	Spleen	Spleen
35	chr2:37499400-37522800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr2:37499400-37528600	Weak transcription	Brain Anterior Caudate	brain
37	chr2:37499400-37540200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr2:37499800-37508400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr2:37500000-37507200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:37500200-37508400	Weak transcription	Brain Germinal Matrix	brain
41	chr2:37500200-37518600	Weak transcription	Fetal Stomach	stomach
42	chr2:37500200-37529800	Weak transcription	Fetal Intestine Small	intestine
43	chr2:37500200-37530200	Weak transcription	Gastric	stomach
44	chr2:37500400-37519200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:37500400-37520400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr2:37500600-37510000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:37500600-37530200	Weak transcription	Thymus	Thymus
48	chr2:37502000-37508200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:37502000-37508400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr2:37502000-37508600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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