Variant report

Variant	rs2227199
Chromosome Location	chr1:172359780-172359781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1011731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1023479	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10489284	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10752943	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10752944	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797996	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10911654	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10911681	0.98[ASN][1000 genomes]
rs10911684	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10911792	0.91[CHB][hapmap]
rs12404665	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12405515	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1894633	0.89[CHB][hapmap]
rs2001127	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001128	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2032528	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2213731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2213732	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2227198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227200	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2269612	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2301453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3213564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3768445	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4471302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4504922	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4916251	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4916252	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4916253	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916254	0.89[ASN][1000 genomes]
rs4916263	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs4916264	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs4916265	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs6424894	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6676665	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6697844	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6698987	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6700575	0.98[ASN][1000 genomes]
rs714515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7517737	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7518039	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7534393	0.96[CEU][hapmap];0.80[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7539464	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539972	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7544610	0.97[ASN][1000 genomes]
rs7546252	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9286854	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425269	1.00[JPT][hapmap]
rs9425291	0.96[CEU][hapmap];0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9425297	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9425298	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425299	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425300	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9425568	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9425579	0.92[ASN][1000 genomes]
rs9425586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9425587	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425589	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425590	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425591	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425628	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs979935	0.90[CHB][hapmap]
rs991790	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2227199	PIGC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172343600-172359800	Weak transcription	Brain Angular Gyrus	brain
2	chr1:172346600-172367400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:172349600-172362000	Weak transcription	Left Ventricle	heart
4	chr1:172349800-172363400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:172350400-172362400	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr1:172350400-172362600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:172351400-172363000	Weak transcription	A549	lung
8	chr1:172351800-172363400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:172352200-172360000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:172352200-172363200	Weak transcription	Fetal Intestine Large	intestine
11	chr1:172352400-172360000	Weak transcription	Primary T cells from cord blood	blood
12	chr1:172352400-172360000	Weak transcription	Small Intestine	intestine
13	chr1:172352400-172386400	Weak transcription	Psoas Muscle	Psoas
14	chr1:172353000-172362600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:172353600-172359800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:172353600-172360000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:172353600-172366400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:172354600-172359800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:172354600-172364000	Weak transcription	Fetal Brain Female	brain
20	chr1:172355000-172363800	Weak transcription	Lung	lung
21	chr1:172355600-172364000	Weak transcription	Fetal Brain Male	brain
22	chr1:172356600-172367400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:172358800-172359800	Enhancers	Primary B cells from peripheral blood	blood
24	chr1:172358800-172359800	Enhancers	Placenta Amnion	Placenta Amnion
25	chr1:172358800-172361400	Enhancers	Fetal Muscle Leg	muscle
26	chr1:172359000-172359800	Enhancers	Primary B cells from cord blood	blood
27	chr1:172359000-172360000	Enhancers	HepG2	liver
28	chr1:172359000-172360400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:172359000-172360400	Enhancers	Brain Cingulate Gyrus	brain
30	chr1:172359000-172360400	Enhancers	Fetal Heart	heart
31	chr1:172359000-172361000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:172359000-172361000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr1:172359200-172359800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr1:172359200-172359800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:172359200-172360000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:172359200-172360000	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr1:172359200-172360400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:172359200-172360600	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr1:172359200-172360800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr1:172359200-172360800	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr1:172359400-172359800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:172359400-172359800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:172359400-172359800	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr1:172359400-172359800	Enhancers	NHDF-Ad	bronchial
45	chr1:172359400-172360000	Enhancers	Aorta	Aorta
46	chr1:172359400-172360000	Enhancers	Brain Anterior Caudate	brain
47	chr1:172359400-172360000	Enhancers	Osteobl	bone
48	chr1:172359400-172360200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:172359400-172360200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr1:172359400-172360200	Genic enhancers	Brain Inferior Temporal Lobe	brain

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