Variant report

Variant	rs9425301
Chromosome Location	chr1:172363815-172363816
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172327680..172330506-chr1:172362622..172365988,3	MCF-7	breast:
2	chr1:172355733..172358323-chr1:172360920..172363821,3	K562	blood:
3	chr1:172362133..172365037-chr1:172367213..172368755,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197959	Chromatin interaction

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[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1023479	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10489284	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10752943	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10752944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10797996	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10911654	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10911681	0.97[ASN][1000 genomes]
rs10911684	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10911792	0.85[CEU][hapmap];0.91[CHB][hapmap]
rs12404665	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12405515	0.89[ASN][1000 genomes]
rs1894633	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs2001127	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2001128	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2001129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2032528	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2213731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2213732	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2227198	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2227199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2227200	0.94[ASN][1000 genomes]
rs2269612	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2301453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3213564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3768445	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4471302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4504922	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4916251	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4916252	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4916253	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4916254	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4916263	0.84[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs4916264	0.84[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs4916265	0.84[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs6424894	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6676665	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6698987	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6700575	0.97[ASN][1000 genomes]
rs714515	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7517737	0.92[ASN][1000 genomes]
rs7518039	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7534393	0.80[CHB][hapmap]
rs7539464	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7539972	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7544610	0.98[ASN][1000 genomes]
rs7546252	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7551242	0.84[CEU][hapmap]
rs9286854	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9425269	1.00[JPT][hapmap]
rs9425291	0.89[CHB][hapmap]
rs9425297	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9425298	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9425299	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9425300	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9425573	0.80[ASN][1000 genomes]
rs9425579	0.93[ASN][1000 genomes]
rs9425586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9425587	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9425589	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9425590	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9425591	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9425592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9425628	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs979935	0.90[CHB][hapmap]
rs991790	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9425301	PIGC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172346600-172367400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:172352400-172386400	Weak transcription	Psoas Muscle	Psoas
3	chr1:172353600-172366400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:172354600-172364000	Weak transcription	Fetal Brain Female	brain
5	chr1:172355600-172364000	Weak transcription	Fetal Brain Male	brain
6	chr1:172356600-172367400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:172360000-172368200	Weak transcription	HepG2	liver
8	chr1:172360200-172364200	Enhancers	Fetal Kidney	kidney
9	chr1:172360200-172368600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:172360200-172369200	Weak transcription	Spleen	Spleen
11	chr1:172360600-172369000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:172360600-172369200	Weak transcription	Small Intestine	intestine
13	chr1:172360800-172365400	Enhancers	Primary B cells from peripheral blood	blood
14	chr1:172361400-172368400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:172361600-172366600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:172361800-172364200	Enhancers	Brain Angular Gyrus	brain
17	chr1:172362000-172364000	Enhancers	Brain Substantia Nigra	brain
18	chr1:172362000-172364000	Flanking Active TSS	GM12878-XiMat	blood
19	chr1:172362000-172364200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:172362000-172364200	Enhancers	Brain Anterior Caudate	brain
21	chr1:172362000-172364600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:172362200-172364200	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr1:172362400-172364400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:172362400-172365000	Enhancers	Primary T cells fromperipheralblood	blood
25	chr1:172362400-172369200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:172362600-172364200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr1:172362600-172368200	Enhancers	Brain Cingulate Gyrus	brain
28	chr1:172362800-172367400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:172362800-172368600	Weak transcription	Left Ventricle	heart
30	chr1:172363000-172364000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr1:172363000-172364200	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr1:172363200-172364000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:172363200-172364000	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr1:172363200-172364000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:172363200-172364000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr1:172363200-172364000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:172363200-172364000	Enhancers	Fetal Stomach	stomach
38	chr1:172363200-172364000	Enhancers	Placenta Amnion	Placenta Amnion
39	chr1:172363200-172364000	Enhancers	Stomach Mucosa	stomach
40	chr1:172363200-172364000	Flanking Active TSS	A549	lung
41	chr1:172363200-172364000	Enhancers	HUVEC	blood vessel
42	chr1:172363200-172364200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr1:172363200-172364200	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr1:172363200-172364200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:172363200-172364200	Enhancers	Muscle Satellite Cultured Cells	--
46	chr1:172363200-172364400	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr1:172363200-172364400	Enhancers	Fetal Intestine Large	intestine
48	chr1:172363200-172365200	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr1:172363200-172365400	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr1:172363400-172364000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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