Variant report

Variant	rs6478092
Chromosome Location	chr9:117381763-117381764
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	HDAC2	chr9:117381485-117382176	MCF-7	breast:	n/a	chr9:117381812-117381831
2	NFATC1	chr9:117381285-117382183	GM12878	blood:	n/a	n/a
3	NRF1	chr9:117381100-117381875	GM12878	blood:	n/a	chr9:117381551-117381565 chr9:117381554-117381565
4	IRF3	chr9:117381708-117382036	GM12878	blood:	n/a	chr9:117381961-117381972 chr9:117381962-117381975 chr9:117381963-117381973 chr9:117381962-117381973 chr9:117381961-117381975 chr9:117381963-117381977 chr9:117381961-117381981 chr9:117381959-117381973 chr9:117381957-117381974 chr9:117381962-117381976 chr9:117381959-117381976
5	PAX5	chr9:117381603-117381974	GM12891	blood:	n/a	chr9:117381906-117381924
6	YY1	chr9:117381746-117382021	GM12878	blood:	n/a	n/a
7	MAX	chr9:117381331-117382056	GM12878	blood:	n/a	n/a
8	WRNIP1	chr9:117381162-117382102	GM12878	blood:	n/a	n/a
9	PAX5	chr9:117381651-117382110	GM12878	blood:	n/a	chr9:117381906-117381924
10	RUNX3	chr9:117381417-117382098	GM12878	blood:	n/a	n/a
11	BHLHE40	chr9:117381378-117382091	GM12878	blood:	n/a	n/a
12	EP300	chr9:117381456-117382100	GM12878	blood:	n/a	chr9:117381958-117381972 chr9:117381739-117381749
13	TAF1	chr9:117381701-117382038	GM12878	blood:	n/a	n/a
14	NR3C1	chr9:117381551-117381876	A549	lung:	n/a	chr9:117381661-117381687 chr9:117381661-117381687 chr9:117381667-117381681 chr9:117381661-117381687 chr9:117381661-117381687 chr9:117381661-117381687
15	SMC3	chr9:117381577-117382089	GM12878	blood:	n/a	n/a
16	POLR2A	chr9:117381753-117381921	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr9:117381557-117382194	GM12878	blood:	n/a	n/a
18	CHD2	chr9:117381496-117382087	GM12878	blood:	n/a	n/a
19	FOXA1	chr9:117381448-117382141	T-47D	breast:	n/a	chr9:117381777-117381792
20	FOXA1	chr9:117381267-117382174	T-47D	breast:	n/a	chr9:117381777-117381792
21	POLR2A	chr9:117381585-117382149	GM12892	blood:	n/a	n/a
22	GATA3	chr9:117381374-117382075	T-47D	breast:	n/a	n/a
23	EP300	chr9:117381414-117382111	T-47D	breast:	n/a	chr9:117381958-117381972 chr9:117381739-117381749
24	EP300	chr9:117381390-117382143	T-47D	breast:	n/a	chr9:117381958-117381972 chr9:117381739-117381749
25	TBP	chr9:117381336-117382134	GM12878	blood:	n/a	n/a
26	NFIC	chr9:117381286-117382172	GM12878	blood:	n/a	n/a
27	ATF2	chr9:117381504-117382095	GM12878	blood:	n/a	n/a
28	FOXA2	chr9:117381609-117381865	HepG2	liver:	n/a	n/a
29	MTA3	chr9:117381038-117382176	GM12878	blood:	n/a	n/a
30	ESR1	chr9:117381395-117382069	T-47D	breast:	n/a	n/a
31	POLR2A	chr9:117381754-117381955	MCF-7	breast:	n/a	n/a
32	ESR1	chr9:117381464-117382103	T-47D	breast:	n/a	n/a
33	MAX	chr9:117381382-117382122	MCF-7	breast:	n/a	n/a
34	GATA3	chr9:117381321-117382050	MCF-7	breast:	n/a	n/a
35	NFIC	chr9:117381308-117382171	GM12878	blood:	n/a	n/a
36	GATA3	chr9:117381383-117382035	T-47D	breast:	n/a	n/a
37	RCOR1	chr9:117381094-117382179	GM12878	blood:	n/a	n/a
38	ESR1	chr9:117381573-117381980	T-47D	breast:	n/a	n/a
39	CHD1	chr9:117381350-117382056	GM12878	blood:	n/a	n/a
40	MXI1	chr9:117381362-117382088	GM12878	blood:	n/a	n/a
41	POLR2A	chr9:117381126-117382145	GM12878	blood:	n/a	n/a
42	EP300	chr9:117381534-117382050	GM12878	blood:	n/a	chr9:117381958-117381972 chr9:117381739-117381749
43	STAT1	chr9:117381522-117382026	GM12878	blood:	n/a	chr9:117381962-117381973
44	FOXM1	chr9:117381608-117382157	GM12878	blood:	n/a	n/a
45	TAF1	chr9:117381723-117382003	GM12892	blood:	n/a	n/a
46	PAX5	chr9:117381577-117382139	GM12878	blood:	n/a	chr9:117381906-117381924
47	IKZF1	chr9:117381486-117382150	GM12878	blood:	n/a	n/a
48	ESR1	chr9:117381479-117382095	T-47D	breast:	n/a	n/a
49	ESR1	chr9:117381490-117382105	T-47D	breast:	n/a	n/a
50	ESR1	chr9:117381488-117382025	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:117249651..117250434-chr9:117381196..117382137,2	MCF-7	breast:
2	chr9:117198028..117200555-chr9:117380478..117382702,2	K562	blood:
3	chr9:117348515..117353806-chr9:117380145..117387168,10	MCF-7	breast:
4	chr9:117379874..117381903-chr9:117388019..117390804,3	K562	blood:
5	chr9:117367243..117369064-chr9:117381451..117383646,2	MCF-7	breast:
6	chr9:117380986..117384351-chr9:117385688..117388944,4	MCF-7	breast:
7	chr9:117164837..117167280-chr9:117381575..117384542,2	MCF-7	breast:
8	chr9:117265529..117267745-chr9:117380597..117382102,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000201749	TF binding region
ENSG00000136888	Chromatin interaction
ENSG00000095397	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10115585	0.85[GIH][hapmap]
rs10739423	0.90[TSI][hapmap];0.81[AMR][1000 genomes]
rs1536737	0.80[TSI][hapmap]
rs4978600	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4978601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4979446	0.90[TSI][hapmap];0.81[AMR][1000 genomes]
rs6478094	0.80[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051544	chr9:116944940-117443031	ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
2	nsv540203	chr9:116944940-117443031	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv1048093	chr9:116945025-117456210	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
4	nsv1050991	chr9:116953739-117442999	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv1046311	chr9:116953739-117447142	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
6	nsv1052877	chr9:116953739-117456210	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv1039681	chr9:116953739-117457158	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
8	nsv1051987	chr9:116955841-117453668	Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
9	nsv1044374	chr9:116955841-117460150	Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
10	nsv466534	chr9:116956268-117455810	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
11	nsv615234	chr9:116956268-117455810	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
12	nsv1048817	chr9:116957958-117456210	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
13	nsv615236	chr9:116958144-117455810	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
14	nsv466535	chr9:116958144-117456175	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
15	nsv615237	chr9:116958144-117456175	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
16	nsv615238	chr9:116958144-117458475	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
17	nsv430094	chr9:116958446-117456446	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
18	nsv1053756	chr9:116975934-117443031	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
19	nsv540204	chr9:116975934-117443031	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
20	nsv1047704	chr9:116978041-117399362	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
21	nsv540205	chr9:116978041-117399362	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
22	nsv530950	chr9:117009156-117399361	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
23	nsv916139	chr9:117009169-117399454	Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
24	nsv530951	chr9:117032675-117439804	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
25	nsv831694	chr9:117328640-117502785	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
26	esv1008480	chr9:117373830-117388680	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117374600-117387800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:117374800-117384000	Weak transcription	NH-A	brain
3	chr9:117374800-117384200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:117374800-117384200	Weak transcription	NHLF	lung
5	chr9:117375000-117384200	Weak transcription	Left Ventricle	heart
6	chr9:117375000-117384200	Weak transcription	Right Atrium	heart
7	chr9:117375000-117384200	Weak transcription	A549	lung
8	chr9:117375000-117384200	Weak transcription	HSMMtube	muscle
9	chr9:117375000-117388800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:117375000-117388800	Weak transcription	Liver	Liver
11	chr9:117375000-117391200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:117375000-117405200	Weak transcription	Psoas Muscle	Psoas
13	chr9:117375000-117410400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr9:117375200-117385600	Weak transcription	Fetal Intestine Small	intestine
15	chr9:117375200-117388800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:117375200-117388800	Weak transcription	Aorta	Aorta
17	chr9:117375200-117388800	Weak transcription	Pancreas	Pancrea
18	chr9:117375200-117389800	Weak transcription	Fetal Brain Male	brain
19	chr9:117375200-117405400	Weak transcription	Small Intestine	intestine
20	chr9:117375400-117389800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr9:117375600-117388800	Weak transcription	Brain Substantia Nigra	brain
22	chr9:117375600-117389600	Weak transcription	Brain Germinal Matrix	brain
23	chr9:117375600-117405400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr9:117375800-117388800	Weak transcription	Fetal Intestine Large	intestine
25	chr9:117375800-117389800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:117375800-117409200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:117375800-117415600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr9:117376000-117384000	Weak transcription	Fetal Brain Female	brain
29	chr9:117376000-117389000	Weak transcription	Brain Hippocampus Middle	brain
30	chr9:117376200-117384200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:117376200-117388800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr9:117376200-117390000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr9:117376200-117390000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr9:117376200-117415600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr9:117376400-117384000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:117376400-117391200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:117376400-117396800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr9:117376600-117396200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr9:117377000-117381800	Weak transcription	Colon Smooth Muscle	Colon
40	chr9:117379000-117382000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:117379200-117384200	Strong transcription	Fetal Stomach	stomach
42	chr9:117379200-117384200	Weak transcription	Lung	lung
43	chr9:117379400-117381800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr9:117379400-117387200	Strong transcription	Stomach Smooth Muscle	stomach
45	chr9:117379400-117390000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr9:117379400-117409600	Strong transcription	Dnd41	blood
47	chr9:117379600-117383600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr9:117379600-117384000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr9:117379600-117384600	Weak transcription	Fetal Muscle Trunk	muscle
50	chr9:117379600-117388600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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