Variant report

Variant	rs16918734
Chromosome Location	chr9:102587049-102587050
allele	G/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	CTCF	chr9:102586980-102587130	Caco-2	colon:	n/a	n/a
2	CTCF	chr9:102586900-102587050	HRE	kidney:	n/a	n/a
3	CTCF	chr9:102586957-102587104	MCF-7	breast:	n/a	n/a
4	MTA3	chr9:102585965-102587422	GM12878	blood:	n/a	n/a
5	RAD21	chr9:102586847-102587232	GM12878	blood:	n/a	chr9:102587209-102587221 chr9:102587211-102587221
6	E2F6	chr9:102586289-102587538	H1-hESC	embryonic stem cell:	n/a	chr9:102586898-102586908 chr9:102587485-102587494
7	RELA	chr9:102586080-102587108	GM18951	blood:	n/a	n/a
8	CTCF	chr9:102586694-102587382	A549	lung:	n/a	n/a
9	CTCF	chr9:102586940-102587090	HAc	cerebellar:	n/a	n/a
10	CTCF	chr9:102586920-102587070	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr9:102586940-102587090	GM12874	blood:	n/a	n/a
12	CTCF	chr9:102586900-102587050	GM12801	blood:	n/a	n/a
13	RAD21	chr9:102586872-102587231	HepG2	liver:	n/a	chr9:102587209-102587221 chr9:102587211-102587221
14	EBF1	chr9:102586017-102587168	GM12878	blood:	n/a	n/a
15	CTCF	chr9:102586913-102587110	GM13976	blood:	n/a	n/a
16	YY1	chr9:102586799-102587236	GM12892	blood:	n/a	n/a
17	CTCF	chr9:102586920-102587070	GM12867	blood:	n/a	n/a
18	CTCF	chr9:102586848-102587294	GM19240	blood:	n/a	n/a
19	CTCF	chr9:102586900-102587050	AG09309	skin:	n/a	n/a
20	CTCF	chr9:102587020-102587170	WI-38	lung:	n/a	n/a
21	CTCF	chr9:102587005-102587063	MCF-7	breast:	n/a	n/a
22	MAX	chr9:102586774-102587186	NB4	blood:	n/a	n/a
23	RAD21	chr9:102586862-102587205	GM12878	blood:	n/a	n/a
24	MAX	chr9:102586264-102587311	GM12878	blood:	n/a	chr9:102586709-102586718 chr9:102586708-102586719 chr9:102586707-102586722 chr9:102586708-102586719
25	CTCF	chr9:102586920-102587070	HCM	heart:	n/a	n/a
26	BACH1	chr9:102586354-102587500	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr9:102586961-102587083	A549	lung:	n/a	n/a
28	CTCF	chr9:102586960-102587110	AG10803	skin:	n/a	n/a
29	CTCF	chr9:102586878-102587313	GM12891	blood:	n/a	n/a
30	RAD21	chr9:102586713-102587515	H1-hESC	embryonic stem cell:	n/a	chr9:102587209-102587221 chr9:102587211-102587221
31	EP300	chr9:102586879-102587130	GM12878	blood:	n/a	n/a
32	POLR2A	chr9:102587011-102587187	H1-hESC	embryonic stem cell:	n/a	n/a
33	TAF1	chr9:102586858-102587406	H1-hESC	embryonic stem cell:	n/a	n/a
34	RAD21	chr9:102586858-102587195	A549	lung:	n/a	n/a
35	PAX5	chr9:102586637-102587138	GM12878	blood:	n/a	chr9:102586867-102586876
36	CTCF	chr9:102586836-102587158	HepG2	liver:	n/a	n/a
37	CTCF	chr9:102586880-102587304	GM12892	blood:	n/a	n/a
38	CHD2	chr9:102586801-102587204	GM12878	blood:	n/a	n/a
39	CTCF	chr9:102586920-102587070	AG10803	skin:	n/a	n/a
40	CTCF	chr9:102586960-102587110	HepG2	liver:	n/a	n/a
41	CTCF	chr9:102586940-102587090	GM12865	blood:	n/a	n/a
42	CTCF	chr9:102586940-102587090	HCPEpiC	choroid plexus:	n/a	n/a
43	RCOR1	chr9:102586852-102587079	K562	blood:	n/a	n/a
44	CTCF	chr9:102586920-102587070	AG04450	lung:	n/a	n/a
45	GABPA	chr9:102586896-102587189	H1-hESC	embryonic stem cell:	n/a	n/a
46	RAD21	chr9:102586742-102587224	A549	lung:	n/a	chr9:102587209-102587221 chr9:102587211-102587221
47	CTCF	chr9:102586933-102587159	Fibrobl	skin:	n/a	n/a
48	CTCF	chr9:102586940-102587090	HEK293	kidney:	n/a	n/a
49	CTCF	chr9:102586960-102587110	SK-N-SH_RA	brain:	n/a	n/a
50	POLR2A	chr9:102586865-102587249	GM12878	blood:	n/a	n/a

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

Variant related genes	Relation type
NR4A3	TF binding region
ENSG00000237461	TF binding region
ENSG00000136874	Chromatin interaction
ENSG00000255145	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	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988895	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10988898	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988904	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988905	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336436	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352835	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1405209	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1417738	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1526265	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918008	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918009	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965564	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2900222	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4742773	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742774	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7019989	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020207	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022059	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026022	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029504	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7029559	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7038780	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041475	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047636	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72744685	0.99[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:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102581200-102587200	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr9:102581200-102587200	Active TSS	NHDF-Ad	bronchial
3	chr9:102581200-102587400	Active TSS	Psoas Muscle	Psoas
4	chr9:102581200-102587800	Active TSS	NHLF	lung
5	chr9:102581400-102587200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:102581400-102587200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:102581400-102587400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr9:102581800-102589800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
9	chr9:102582600-102588000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:102583000-102588200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr9:102583600-102587200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:102583600-102587400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr9:102584200-102587400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
14	chr9:102584400-102587400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
15	chr9:102584400-102587400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
16	chr9:102584400-102587400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
17	chr9:102584400-102587600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
18	chr9:102584400-102587600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
19	chr9:102584600-102587200	Active TSS	Right Atrium	heart
20	chr9:102584600-102587400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
21	chr9:102584600-102587600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
22	chr9:102584600-102587600	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr9:102584600-102587600	Flanking Bivalent TSS/Enh	Thymus	Thymus
24	chr9:102584600-102588200	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
25	chr9:102584600-102588400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
26	chr9:102584800-102587400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
27	chr9:102584800-102587600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
28	chr9:102584800-102588200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr9:102584800-102588400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
30	chr9:102585000-102588000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr9:102585200-102587600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
32	chr9:102585200-102588400	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
33	chr9:102585200-102588400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr9:102585200-102590200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
35	chr9:102585400-102587600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:102585400-102588200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr9:102585600-102587400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:102585600-102587600	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr9:102585600-102588200	Enhancers	Spleen	Spleen
40	chr9:102585800-102587400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
41	chr9:102585800-102587600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
42	chr9:102585800-102588000	Bivalent Enhancer	Small Intestine	intestine
43	chr9:102585800-102588200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
44	chr9:102586000-102588200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
45	chr9:102586000-102589000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
46	chr9:102586200-102587200	Flanking Active TSS	GM12878-XiMat	blood
47	chr9:102586200-102587400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr9:102586200-102587400	Flanking Bivalent TSS/Enh	Placenta	Placenta
49	chr9:102586200-102587400	Flanking Active TSS	Pancreas	Pancrea
50	chr9:102586200-102587400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum

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