Variant report

Variant	rs9425291
Chromosome Location	chr1:172312769-172312770
allele	A/G
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	BATF	chr1:172312541-172312864	GM12878	blood:	n/a	n/a
2	FOS	chr1:172312658-172313258	MCF10A-Er-Src	breast:	n/a	chr1:172313071-172313082 chr1:172313074-172313085 chr1:172313075-172313084 chr1:172313073-172313084
3	FOS	chr1:172312557-172313230	Hela-S3	cervix:	n/a	chr1:172313071-172313082 chr1:172313074-172313085 chr1:172313075-172313084 chr1:172313073-172313084
4	BHLHE40	chr1:172311609-172313011	GM12878	blood:	n/a	n/a
5	ZNF384	chr1:172311628-172313309	GM12878	blood:	n/a	chr1:172312806-172312814
6	POLR2A	chr1:172312531-172312817	Hela-S3	cervix:	n/a	n/a
7	FOS	chr1:172312592-172313267	MCF10A-Er-Src	breast:	n/a	chr1:172313071-172313082 chr1:172313074-172313085 chr1:172313075-172313084 chr1:172313073-172313084
8	STAT3	chr1:172312735-172313210	MCF10A-Er-Src	breast:	n/a	chr1:172313075-172313084 chr1:172312908-172312928
9	POLR2A	chr1:172312511-172313354	SK-N-SH	brain:	n/a	n/a
10	ESR1	chr1:172312482-172312831	ECC-1	luminal epithelium:	n/a	n/a
11	EP300	chr1:172312300-172313524	SK-N-SH	brain:	n/a	chr1:172312483-172312497 chr1:172312532-172312546
12	IKZF1	chr1:172311698-172313140	GM12878	blood:	n/a	n/a
13	FOSL2	chr1:172312409-172313368	SK-N-SH	brain:	n/a	chr1:172313071-172313082 chr1:172313074-172313085 chr1:172313075-172313084
14	NFIC	chr1:172311456-172313087	GM12878	blood:	n/a	n/a
15	TAF1	chr1:172312554-172312825	SK-N-SH	brain:	n/a	n/a
16	JUND	chr1:172312437-172313482	SK-N-SH	brain:	n/a	chr1:172313360-172313369 chr1:172313071-172313082 chr1:172313074-172313085 chr1:172313467-172313475 chr1:172313075-172313084 chr1:172313073-172313084
17	TCF12	chr1:172312314-172313540	SK-N-SH	brain:	n/a	chr1:172312769-172312776 chr1:172312549-172312559
18	RELA	chr1:172311559-172313226	GM12878	blood:	n/a	chr1:172312908-172312917 chr1:172312908-172312917
19	TEAD4	chr1:172312402-172313408	SK-N-SH	brain:	n/a	n/a
20	TBP	chr1:172311549-172313162	GM12878	blood:	n/a	n/a
21	JUND	chr1:172312519-172313362	Hela-S3	cervix:	n/a	chr1:172313071-172313082 chr1:172313074-172313085 chr1:172313075-172313084 chr1:172313073-172313084
22	POLR2A	chr1:172312420-172313364	HUVEC	blood vessel:	n/a	n/a
23	PBX3	chr1:172312416-172313437	SK-N-SH	brain:	n/a	chr1:172313361-172313370
24	JUND	chr1:172312341-172313478	SK-N-SH	brain:	n/a	chr1:172313360-172313369 chr1:172313071-172313082 chr1:172313074-172313085 chr1:172313467-172313475 chr1:172313075-172313084 chr1:172313073-172313084
25	PBX3	chr1:172312300-172313370	SK-N-SH	brain:	n/a	chr1:172313361-172313370
26	FOS	chr1:172312593-172313249	MCF10A-Er-Src	breast:	n/a	chr1:172313071-172313082 chr1:172313074-172313085 chr1:172313075-172313084 chr1:172313073-172313084
27	FOS	chr1:172312592-172313237	MCF10A-Er-Src	breast:	n/a	chr1:172313071-172313082 chr1:172313074-172313085 chr1:172313075-172313084 chr1:172313073-172313084
28	ATF2	chr1:172311381-172313278	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:172312555-172313225	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr1:172312463-172313010	MCF10A-Er-Src	breast:	n/a	n/a
31	TCF12	chr1:172312444-172313470	ECC-1	luminal epithelium:	n/a	chr1:172312769-172312776 chr1:172312549-172312559
32	FOXM1	chr1:172312432-172313563	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr1:172312498-172312896	GM12878	blood:	n/a	n/a
34	SMC3	chr1:172312551-172313380	GM12878	blood:	n/a	n/a
35	EP300	chr1:172312477-172313483	ECC-1	luminal epithelium:	n/a	chr1:172312483-172312497 chr1:172312532-172312546
36	SPI1	chr1:172312295-172312783	GM12891	blood:	n/a	chr1:172312488-172312497
37	CHD1	chr1:172311799-172313706	GM12878	blood:	n/a	n/a
38	RAD21	chr1:172312527-172312821	SK-N-SH_RA	brain:	n/a	n/a
39	RCOR1	chr1:172311706-172312851	GM12878	blood:	n/a	n/a
40	STAT3	chr1:172311785-172313192	GM12878	blood:	n/a	chr1:172313075-172313084 chr1:172312488-172312499 chr1:172312908-172312928
41	YY1	chr1:172312498-172312797	SK-N-SH_RA	brain:	n/a	n/a
42	RELA	chr1:172311731-172313287	GM19099	blood:	n/a	chr1:172312908-172312917 chr1:172312908-172312917
43	NFIC	chr1:172312387-172313537	SK-N-SH	brain:	n/a	chr1:172313123-172313151
44	EP300	chr1:172311564-172313542	GM12878	blood:	n/a	chr1:172312483-172312497 chr1:172312532-172312546 chr1:172312006-172312020 chr1:172311883-172311893 chr1:172312010-172312019
45	RAD21	chr1:172312610-172313330	IMR90	lung:	n/a	n/a
46	GATA3	chr1:172312346-172313428	SK-N-SH	brain:	n/a	chr1:172312995-172313004
47	PAX5	chr1:172312570-172312848	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:172312494-172313361	HUVEC	blood vessel:	n/a	n/a
49	ZNF143	chr1:172312596-172312982	GM12878	blood:	n/a	n/a
50	USF2	chr1:172312549-172313300	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172305536..172310300-chr1:172311582..172315417,5	K562	blood:

Variant related genes	Relation type
ENSG00000252354	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1011731	0.93[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1023479	0.89[CHB][hapmap]
rs10489284	0.89[CHB][hapmap]
rs10752943	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10752944	0.89[CEU][hapmap];0.89[CHB][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10797996	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10911684	0.89[CHB][hapmap]
rs12404665	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12405515	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1894633	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2001127	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2001128	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2001129	0.96[CEU][hapmap];0.89[CHB][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2032528	0.88[CHB][hapmap]
rs2213731	0.89[CHB][hapmap]
rs2213732	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2227198	0.87[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2227199	0.96[CEU][hapmap];0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2227200	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2269612	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2301453	0.93[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3213564	0.89[CHB][hapmap]
rs34945663	0.81[ASN][1000 genomes]
rs3768445	0.89[CHB][hapmap]
rs4471302	0.89[CHB][hapmap]
rs4916251	0.89[CHB][hapmap]
rs4916252	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4916253	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57668887	0.96[ASN][1000 genomes]
rs6424894	0.89[CHB][hapmap]
rs6676665	0.89[CHB][hapmap]
rs6697844	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698987	0.89[CHB][hapmap]
rs714515	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]
rs73046851	0.93[ASN][1000 genomes]
rs7517737	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7534393	1.00[CEU][hapmap];0.89[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]
rs7539464	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7546252	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9286854	0.89[CEU][hapmap];0.89[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9425297	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9425298	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9425299	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9425300	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9425301	0.89[CHB][hapmap]
rs9425568	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425573	0.95[ASN][1000 genomes]
rs9425575	0.93[ASN][1000 genomes]
rs9425586	0.89[CHB][hapmap]
rs9425587	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9425589	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9425590	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9425591	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9425592	0.93[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9425628	0.88[CHB][hapmap]
rs979935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs991790	0.96[CEU][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9425291	PIGC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172308000-172313200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr1:172309200-172313800	Enhancers	Primary B cells from peripheral blood	blood
3	chr1:172310600-172313800	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr1:172310800-172313600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr1:172311000-172313200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:172311000-172313600	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr1:172311200-172312800	Enhancers	NHDF-Ad	bronchial
8	chr1:172311200-172313200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr1:172311200-172313400	Enhancers	Brain Hippocampus Middle	brain
10	chr1:172311200-172314800	Enhancers	Fetal Kidney	kidney
11	chr1:172311400-172312800	Enhancers	Brain Cingulate Gyrus	brain
12	chr1:172311400-172313000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr1:172311400-172313000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:172311400-172313800	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr1:172311600-172312800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr1:172311600-172312800	Enhancers	Primary B cells from cord blood	blood
17	chr1:172311600-172312800	Enhancers	Fetal Lung	lung
18	chr1:172311600-172313400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:172311600-172313400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:172311600-172313400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr1:172311600-172313400	Enhancers	Brain Angular Gyrus	brain
22	chr1:172311600-172313600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:172311600-172313600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:172311600-172313600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:172311600-172313800	Enhancers	HMEC	breast
26	chr1:172311800-172313800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:172311800-172314000	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr1:172312000-172312800	Enhancers	A549	lung
29	chr1:172312000-172313400	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr1:172312000-172313600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr1:172312000-172313800	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr1:172312000-172313800	Flanking Active TSS	GM12878-XiMat	blood
33	chr1:172312000-172314000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:172312000-172314000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:172312000-172314000	Enhancers	Colon Smooth Muscle	Colon
36	chr1:172312000-172314000	Enhancers	Fetal Stomach	stomach
37	chr1:172312200-172312800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:172312200-172312800	Enhancers	Fetal Intestine Small	intestine
39	chr1:172312200-172312800	Flanking Active TSS	HSMMtube	muscle
40	chr1:172312200-172313000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:172312200-172313200	Weak transcription	Stomach Mucosa	stomach
42	chr1:172312200-172313400	Enhancers	Primary hematopoietic stem cells	blood
43	chr1:172312200-172313400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:172312200-172313400	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr1:172312200-172313400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:172312200-172313400	Flanking Active TSS	Hela-S3	cervix
47	chr1:172312200-172313600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:172312200-172313600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr1:172312200-172313800	Enhancers	Adipose Nuclei	Adipose
50	chr1:172312200-172314000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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