Variant report

Variant	rs10489286
Chromosome Location	chr1:172312919-172312920
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	FOS	chr1:172312658-172313258	MCF10A-Er-Src	breast:	n/a	chr1:172313071-172313082 chr1:172313074-172313085 chr1:172313075-172313084 chr1:172313073-172313084
2	FOS	chr1:172312557-172313230	Hela-S3	cervix:	n/a	chr1:172313071-172313082 chr1:172313074-172313085 chr1:172313075-172313084 chr1:172313073-172313084
3	BHLHE40	chr1:172311609-172313011	GM12878	blood:	n/a	n/a
4	ZNF384	chr1:172311628-172313309	GM12878	blood:	n/a	chr1:172312806-172312814
5	JUND	chr1:172312910-172313298	H1-hESC	embryonic stem cell:	n/a	chr1:172313071-172313082 chr1:172313074-172313085 chr1:172313075-172313084 chr1:172313073-172313084
6	MYC	chr1:172312889-172313135	MCF10A-Er-Src	breast:	n/a	chr1:172313074-172313083
7	STAT3	chr1:172312838-172313492	MCF10A-Er-Src	breast:	n/a	chr1:172313075-172313084 chr1:172312908-172312928
8	FOS	chr1:172312592-172313267	MCF10A-Er-Src	breast:	n/a	chr1:172313071-172313082 chr1:172313074-172313085 chr1:172313075-172313084 chr1:172313073-172313084
9	STAT3	chr1:172312735-172313210	MCF10A-Er-Src	breast:	n/a	chr1:172313075-172313084 chr1:172312908-172312928
10	POLR2A	chr1:172312511-172313354	SK-N-SH	brain:	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	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
16	TCF12	chr1:172312314-172313540	SK-N-SH	brain:	n/a	chr1:172312769-172312776 chr1:172312549-172312559
17	RELA	chr1:172311559-172313226	GM12878	blood:	n/a	chr1:172312908-172312917 chr1:172312908-172312917
18	TEAD4	chr1:172312402-172313408	SK-N-SH	brain:	n/a	n/a
19	TBP	chr1:172311549-172313162	GM12878	blood:	n/a	n/a
20	JUND	chr1:172312519-172313362	Hela-S3	cervix:	n/a	chr1:172313071-172313082 chr1:172313074-172313085 chr1:172313075-172313084 chr1:172313073-172313084
21	POLR2A	chr1:172312420-172313364	HUVEC	blood vessel:	n/a	n/a
22	PBX3	chr1:172312416-172313437	SK-N-SH	brain:	n/a	chr1:172313361-172313370
23	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
24	STAT3	chr1:172312890-172313201	MCF10A-Er-Src	breast:	n/a	chr1:172313075-172313084 chr1:172312908-172312928
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	JUND	chr1:172312821-172313376	HCT-116	colon:	n/a	chr1:172313360-172313369 chr1:172313071-172313082 chr1:172313074-172313085 chr1:172313075-172313084 chr1:172313073-172313084
32	TCF12	chr1:172312444-172313470	ECC-1	luminal epithelium:	n/a	chr1:172312769-172312776 chr1:172312549-172312559
33	FOXM1	chr1:172312432-172313563	ECC-1	luminal epithelium:	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	CHD1	chr1:172311799-172313706	GM12878	blood:	n/a	n/a
37	STAT3	chr1:172311785-172313192	GM12878	blood:	n/a	chr1:172313075-172313084 chr1:172312488-172312499 chr1:172312908-172312928
38	RELA	chr1:172311731-172313287	GM19099	blood:	n/a	chr1:172312908-172312917 chr1:172312908-172312917
39	NFIC	chr1:172312387-172313537	SK-N-SH	brain:	n/a	chr1:172313123-172313151
40	STAT3	chr1:172312873-172313207	MCF10A-Er-Src	breast:	n/a	chr1:172313075-172313084 chr1:172312908-172312928
41	EP300	chr1:172311564-172313542	GM12878	blood:	n/a	chr1:172312483-172312497 chr1:172312532-172312546 chr1:172312006-172312020 chr1:172311883-172311893 chr1:172312010-172312019
42	RAD21	chr1:172312610-172313330	IMR90	lung:	n/a	n/a
43	GATA3	chr1:172312346-172313428	SK-N-SH	brain:	n/a	chr1:172312995-172313004
44	POLR2A	chr1:172312494-172313361	HUVEC	blood vessel:	n/a	n/a
45	ZNF143	chr1:172312596-172312982	GM12878	blood:	n/a	n/a
46	USF2	chr1:172312549-172313300	Hela-S3	cervix:	n/a	n/a
47	EP300	chr1:172311684-172313875	GM12878	blood:	n/a	chr1:172312483-172312497 chr1:172312532-172312546 chr1:172312006-172312020 chr1:172311883-172311893 chr1:172312010-172312019
48	NFIC	chr1:172311293-172313258	GM12878	blood:	n/a	chr1:172313123-172313151
49	GATA3	chr1:172312026-172313506	SK-N-SH	brain:	n/a	chr1:172312995-172313004
50	IRF4	chr1:172312389-172312954	GM12878	blood:	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: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1052256	1.00[ASN][1000 genomes]
rs10752953	1.00[ASN][1000 genomes]
rs1132148	1.00[ASN][1000 genomes]
rs12031216	1.00[ASN][1000 genomes]
rs17277918	0.95[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17277932	1.00[ASN][1000 genomes]
rs17368942	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17369011	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422139	1.00[ASN][1000 genomes]
rs4916185	1.00[ASN][1000 genomes]
rs4916255	1.00[ASN][1000 genomes]
rs4916256	1.00[ASN][1000 genomes]
rs56259646	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56340136	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61806074	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61806089	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61806090	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61806091	1.00[ASN][1000 genomes]
rs6660051	1.00[ASN][1000 genomes]
rs6674018	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425307	1.00[ASN][1000 genomes]
rs9425309	1.00[ASN][1000 genomes]
rs9425314	1.00[ASN][1000 genomes]
rs9425315	1.00[ASN][1000 genomes]
rs9425610	1.00[ASN][1000 genomes]
rs978875	1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10489286	GORAB	cis	parietal	SCAN

Chromatin state (count:76 , 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	chr1:172311200-172313200	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr1:172311200-172313400	Enhancers	Brain Hippocampus Middle	brain
9	chr1:172311200-172314800	Enhancers	Fetal Kidney	kidney
10	chr1:172311400-172313000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr1:172311400-172313000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:172311400-172313800	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr1:172311600-172313400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:172311600-172313400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:172311600-172313400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr1:172311600-172313400	Enhancers	Brain Angular Gyrus	brain
17	chr1:172311600-172313600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:172311600-172313600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:172311600-172313600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:172311600-172313800	Enhancers	HMEC	breast
21	chr1:172311800-172313800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:172311800-172314000	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr1:172312000-172313400	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr1:172312000-172313600	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr1:172312000-172313800	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr1:172312000-172313800	Flanking Active TSS	GM12878-XiMat	blood
27	chr1:172312000-172314000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:172312000-172314000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:172312000-172314000	Enhancers	Colon Smooth Muscle	Colon
30	chr1:172312000-172314000	Enhancers	Fetal Stomach	stomach
31	chr1:172312200-172313000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:172312200-172313200	Weak transcription	Stomach Mucosa	stomach
33	chr1:172312200-172313400	Enhancers	Primary hematopoietic stem cells	blood
34	chr1:172312200-172313400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:172312200-172313400	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr1:172312200-172313400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:172312200-172313400	Flanking Active TSS	Hela-S3	cervix
38	chr1:172312200-172313600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:172312200-172313600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr1:172312200-172313800	Enhancers	Adipose Nuclei	Adipose
41	chr1:172312200-172314000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:172312200-172314600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr1:172312400-172313000	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr1:172312400-172313000	Flanking Active TSS	NH-A	brain
45	chr1:172312400-172313400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:172312400-172313800	Flanking Active TSS	NHLF	lung
47	chr1:172312600-172313000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr1:172312600-172313000	Enhancers	Primary T cells from cord blood	blood
49	chr1:172312600-172313000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:172312600-172313000	Flanking Active TSS	Fetal Muscle Leg	muscle

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