Variant report

Variant	rs714515
Chromosome Location	chr1:172352990-172352991
allele	C/T
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	FOXA1	chr1:172352807-172353023	T-47D	breast:	n/a	n/a
2	GATA3	chr1:172352742-172353044	T-47D	breast:	n/a	n/a
3	GATA3	chr1:172352679-172353183	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr1:172352587-172353208	SK-N-SH	brain:	n/a	n/a
5	FOXA1	chr1:172352772-172353065	T-47D	breast:	n/a	n/a
6	JUND	chr1:172352696-172353055	SK-N-SH	brain:	n/a	n/a
7	ESR1	chr1:172352733-172353029	T-47D	breast:	n/a	n/a
8	TEAD4	chr1:172352656-172353187	ECC-1	luminal epithelium:	n/a	chr1:172352911-172352920
9	POLR2A	chr1:172352739-172353028	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:172352695..172354230-chr1:172354543..172357309,2	K562	blood:
2	chr1:172345198..172346938-chr1:172350887..172353536,2	K562	blood:
3	chr1:172352277..172354230-chr1:172354543..172356133,2	K562	blood:

Variant related genes	Relation type
PIGC	TF binding region
DNM3	TF binding region
ENSG00000197959	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1011731	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1023479	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10489284	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10752943	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10752944	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10797996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911654	0.84[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10911681	0.95[ASN][1000 genomes]
rs10911684	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10911792	0.89[CHB][hapmap]
rs12404665	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12405515	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1894633	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs2001127	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2001128	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2001129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2032528	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2213731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2213732	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227198	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2227199	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]
rs2227200	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2269612	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301453	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213564	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3768445	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4471302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4504922	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4916251	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4916252	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916253	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4916254	0.86[ASN][1000 genomes]
rs4916263	0.89[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs4916264	0.89[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs4916265	0.89[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs57668887	0.81[ASN][1000 genomes]
rs6424894	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6676665	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6697844	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6698987	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6700575	0.95[ASN][1000 genomes]
rs73046851	0.81[ASN][1000 genomes]
rs7517737	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7518039	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7534393	0.96[CEU][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7539464	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7539972	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7544610	0.93[ASN][1000 genomes]
rs7546252	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9286854	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425269	1.00[JPT][hapmap]
rs9425291	0.93[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.98[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9425297	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9425298	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425299	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425300	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9425568	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9425573	0.82[ASN][1000 genomes]
rs9425575	0.81[ASN][1000 genomes]
rs9425579	0.95[ASN][1000 genomes]
rs9425586	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9425587	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425590	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9425591	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425592	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425628	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs979935	0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs991790	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs714515	PIGC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 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	chr1:172344800-172357800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:172344800-172359000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:172346600-172367400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:172347400-172357600	Weak transcription	Brain Substantia Nigra	brain
6	chr1:172348600-172353600	Enhancers	Fetal Lung	lung
7	chr1:172349600-172353600	Enhancers	Fetal Stomach	stomach
8	chr1:172349600-172353800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:172349600-172356400	Enhancers	Fetal Kidney	kidney
10	chr1:172349600-172362000	Weak transcription	Left Ventricle	heart
11	chr1:172349800-172353600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:172349800-172353800	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:172349800-172353800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr1:172349800-172363400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:172350000-172354000	Enhancers	Fetal Muscle Leg	muscle
16	chr1:172350200-172353800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr1:172350400-172353000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:172350400-172353200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:172350400-172353800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:172350400-172354400	Weak transcription	Thymus	Thymus
21	chr1:172350400-172357600	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:172350400-172359400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:172350400-172362400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr1:172350400-172362600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:172350800-172354200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr1:172351000-172353000	Active TSS	Aorta	Aorta
27	chr1:172351000-172353600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:172351000-172353600	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr1:172351000-172354000	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr1:172351200-172354000	Enhancers	Placenta Amnion	Placenta Amnion
31	chr1:172351200-172354200	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr1:172351400-172353800	Enhancers	H1 Cell Line	embryonic stem cell
33	chr1:172351400-172353800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:172351400-172354000	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr1:172351400-172356800	Weak transcription	Fetal Intestine Small	intestine
36	chr1:172351400-172357800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:172351400-172363000	Weak transcription	A549	lung
38	chr1:172351600-172353800	Enhancers	Fetal Heart	heart
39	chr1:172351800-172353400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:172351800-172353400	Enhancers	Primary hematopoietic stem cells	blood
41	chr1:172351800-172354200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:172351800-172359400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:172351800-172363400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr1:172352000-172353600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:172352000-172353800	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr1:172352000-172353800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:172352000-172353800	Enhancers	Muscle Satellite Cultured Cells	--
48	chr1:172352000-172353800	Enhancers	NH-A	brain
49	chr1:172352200-172353000	Flanking Active TSS	Rectal Smooth Muscle	rectum
50	chr1:172352200-172353600	Enhancers	HSMM	muscle

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