Variant report

Variant	rs1918009
Chromosome Location	chr9:102586048-102586049
allele	C/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	EGR1	chr9:102586017-102586337	GM12878	blood:	n/a	chr9:102586175-102586185 chr9:102586175-102586184 chr9:102586174-102586184 chr9:102586174-102586187 chr9:102586173-102586187 chr9:102586171-102586185 chr9:102586174-102586187 chr9:102586174-102586187 chr9:102586169-102586191 chr9:102586174-102586187 chr9:102586173-102586188 chr9:102586157-102586170
2	MTA3	chr9:102585965-102587422	GM12878	blood:	n/a	n/a
3	EGR1	chr9:102585938-102586364	K562	blood:	n/a	chr9:102586175-102586185 chr9:102586012-102586025 chr9:102586175-102586184 chr9:102586174-102586184 chr9:102586174-102586187 chr9:102586173-102586187 chr9:102586171-102586185 chr9:102586174-102586187 chr9:102586174-102586187 chr9:102586169-102586191 chr9:102586174-102586187 chr9:102586173-102586188 chr9:102586157-102586170
4	EBF1	chr9:102586017-102587168	GM12878	blood:	n/a	n/a
5	EGR1	chr9:102585899-102586479	MCF-7	breast:	n/a	chr9:102586175-102586185 chr9:102586012-102586025 chr9:102586175-102586184 chr9:102586174-102586184 chr9:102586174-102586187 chr9:102586173-102586187 chr9:102586171-102586185 chr9:102586174-102586187 chr9:102586174-102586187 chr9:102586169-102586191 chr9:102586174-102586187 chr9:102586173-102586188 chr9:102586157-102586170
6	MXI1	chr9:102580459-102586751	SK-N-SH	brain:	n/a	chr9:102585006-102585021
7	EGR1	chr9:102586023-102586434	H1-hESC	embryonic stem cell:	n/a	chr9:102586175-102586185 chr9:102586175-102586184 chr9:102586174-102586184 chr9:102586174-102586187 chr9:102586173-102586187 chr9:102586171-102586185 chr9:102586174-102586187 chr9:102586174-102586187 chr9:102586169-102586191 chr9:102586174-102586187 chr9:102586173-102586188 chr9:102586157-102586170
8	HCFC1	chr9:102581313-102586195	Hela-S3	cervix:	n/a	n/a
9	MXI1	chr9:102582345-102587220	IMR90	lung:	n/a	chr9:102585006-102585021
10	POLR2A	chr9:102580651-102615596	IMR90	lung:	n/a	n/a
11	RUNX3	chr9:102585871-102587227	GM12878	blood:	n/a	n/a
12	POLR2A	chr9:102586033-102586473	GM12891	blood:	n/a	n/a
13	EGR1	chr9:102585933-102586451	ECC-1	luminal epithelium:	n/a	chr9:102586175-102586185 chr9:102586012-102586025 chr9:102586175-102586184 chr9:102586174-102586184 chr9:102586174-102586187 chr9:102586173-102586187 chr9:102586171-102586185 chr9:102586174-102586187 chr9:102586174-102586187 chr9:102586169-102586191 chr9:102586174-102586187 chr9:102586173-102586188 chr9:102586157-102586170
14	ATF2	chr9:102585994-102586466	GM12878	blood:	n/a	n/a
15	POLR2A	chr9:102586045-102587469	GM19193	blood:	n/a	n/a
16	SUZ12	chr9:102584043-102587959	NT2-D1	testis:	n/a	n/a
17	EGR1	chr9:102586033-102586393	GM12878	blood:	n/a	chr9:102586175-102586185 chr9:102586175-102586184 chr9:102586174-102586184 chr9:102586174-102586187 chr9:102586173-102586187 chr9:102586171-102586185 chr9:102586174-102586187 chr9:102586174-102586187 chr9:102586169-102586191 chr9:102586174-102586187 chr9:102586173-102586188 chr9:102586157-102586170
18	YY1	chr9:102586038-102586529	GM12892	blood:	n/a	chr9:102586375-102586386 chr9:102586372-102586386 chr9:102586369-102586383
19	EGR1	chr9:102585984-102586382	K562	blood:	n/a	chr9:102586175-102586185 chr9:102586012-102586025 chr9:102586175-102586184 chr9:102586174-102586184 chr9:102586174-102586187 chr9:102586173-102586187 chr9:102586171-102586185 chr9:102586174-102586187 chr9:102586174-102586187 chr9:102586169-102586191 chr9:102586174-102586187 chr9:102586173-102586188 chr9:102586157-102586170
20	POLR2A	chr9:102586035-102586571	GM12891	blood:	n/a	n/a
21	MAZ	chr9:102585071-102586330	Hela-S3	cervix:	n/a	n/a
22	MAZ	chr9:102586021-102586376	K562	blood:	n/a	n/a
23	PML	chr9:102586003-102587255	GM12878	blood:	n/a	n/a
24	RELA	chr9:102585956-102587328	GM12891	blood:	n/a	n/a
25	FOXM1	chr9:102585987-102586501	GM12878	blood:	n/a	n/a
26	NFIC	chr9:102585956-102586483	GM12878	blood:	n/a	n/a
27	POLR2A	chr9:102581353-102588486	H1-neurons	neurons:	n/a	n/a
28	RUNX3	chr9:102585947-102587291	GM12878	blood:	n/a	n/a
29	POLR2A	chr9:102581348-102586539	Hela-S3	cervix:	n/a	n/a
30	YY1	chr9:102586024-102586410	GM12878	blood:	n/a	chr9:102586375-102586386 chr9:102586372-102586386 chr9:102586369-102586383
31	CHD1	chr9:102580653-102589546	IMR90	lung:	n/a	chr9:102582518-102582528
32	STAT5A	chr9:102585967-102586663	GM12878	blood:	n/a	chr9:102586142-102586154
33	ELF1	chr9:102585942-102587355	GM12878	blood:	n/a	chr9:102586887-102586899 chr9:102586367-102586379
34	MAZ	chr9:102580615-102587613	IMR90	lung:	n/a	chr9:102582833-102582843 chr9:102586709-102586718 chr9:102583341-102583348 chr9:102586708-102586719 chr9:102582184-102582194 chr9:102581879-102581888 chr9:102586707-102586722 chr9:102585006-102585015 chr9:102587483-102587493 chr9:102586708-102586719
35	MAZ	chr9:102585699-102587245	GM12878	blood:	n/a	chr9:102586709-102586718 chr9:102586708-102586719 chr9:102586707-102586722 chr9:102586708-102586719
36	EGR1	chr9:102585977-102586428	ECC-1	luminal epithelium:	n/a	chr9:102586175-102586185 chr9:102586012-102586025 chr9:102586175-102586184 chr9:102586174-102586184 chr9:102586174-102586187 chr9:102586173-102586187 chr9:102586171-102586185 chr9:102586174-102586187 chr9:102586174-102586187 chr9:102586169-102586191 chr9:102586174-102586187 chr9:102586173-102586188 chr9:102586157-102586170

No.	Distal block	Cell Line	Cell type
1	chr9:101983020..101985403-chr9:102581774..102586122,4	MCF-7	breast:
2	chr9:102584673..102587915-chr9:102597686..102600720,3	MCF-7	breast:
3	chr9:102580555..102587852-chr9:102667958..102670918,11	MCF-7	breast:
4	chr9:102580482..102589062-chr9:102666380..102672134,16	MCF-7	breast:

Variant related genes	Relation type
NR4A3	TF binding region
ENSG00000237461	TF binding region
ENSG00000255145	Chromatin interaction
ENSG00000136874	Chromatin interaction
ENSG00000119523	Chromatin interaction
ENSG00000106803	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10156557	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988895	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10988898	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988904	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988905	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336436	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352835	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1405209	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1417738	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1526265	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16918734	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918008	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965564	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2900222	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4742773	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742774	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7019989	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020207	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022059	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026022	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029504	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7029559	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7038780	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041475	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047636	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72744685	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv528025	chr9:102540386-102613672	Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv893622	chr9:102543355-102595685	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv831668	chr9:102568169-102747293	Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102580800-102586800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:102581000-102586400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr9:102581200-102586200	Active TSS	Hela-S3	cervix
4	chr9:102581200-102587200	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr9:102581200-102587200	Active TSS	NHDF-Ad	bronchial
6	chr9:102581200-102587400	Active TSS	Psoas Muscle	Psoas
7	chr9:102581200-102587800	Active TSS	NHLF	lung
8	chr9:102581400-102586400	Active TSS	Brain Cingulate Gyrus	brain
9	chr9:102581400-102586600	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr9:102581400-102586600	Active TSS	Left Ventricle	heart
11	chr9:102581400-102586600	Active TSS	Ovary	ovary
12	chr9:102581400-102586800	Active TSS	Aorta	Aorta
13	chr9:102581400-102586800	Active TSS	Colon Smooth Muscle	Colon
14	chr9:102581400-102587000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:102581400-102587000	Active TSS	A549	lung
16	chr9:102581400-102587200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:102581400-102587200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:102581400-102587400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr9:102581600-102586200	Active TSS	Lung	lung
20	chr9:102581600-102586400	Active TSS	Brain Anterior Caudate	brain
21	chr9:102581600-102586600	Active TSS	Brain Hippocampus Middle	brain
22	chr9:102581600-102586600	Active TSS	Gastric	stomach
23	chr9:102581800-102589800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
24	chr9:102582400-102586600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
25	chr9:102582600-102588000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr9:102583000-102588200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
27	chr9:102583200-102586400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:102583200-102586400	Active TSS	HSMM	muscle
29	chr9:102583400-102586600	Active TSS	Fetal Heart	heart
30	chr9:102583600-102587200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:102583600-102587400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
32	chr9:102584200-102586600	Flanking Active TSS	Liver	Liver
33	chr9:102584200-102587400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
34	chr9:102584400-102586600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
35	chr9:102584400-102587400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
36	chr9:102584400-102587400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
37	chr9:102584400-102587400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
38	chr9:102584400-102587600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
39	chr9:102584400-102587600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
40	chr9:102584600-102586600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr9:102584600-102587000	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 1	blood
42	chr9:102584600-102587200	Active TSS	Right Atrium	heart
43	chr9:102584600-102587400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
44	chr9:102584600-102587600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
45	chr9:102584600-102587600	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr9:102584600-102587600	Flanking Bivalent TSS/Enh	Thymus	Thymus
47	chr9:102584600-102588200	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
48	chr9:102584600-102588400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
49	chr9:102584800-102586200	Bivalent/Poised TSS	Fetal Kidney	kidney
50	chr9:102584800-102586400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum

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