Variant report

Variant	rs41278667
Chromosome Location	chr9:117379589-117379590
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	EBF1	chr9:117378920-117379762	GM12878	blood:	n/a	chr9:117379231-117379242
2	TCF12	chr9:117379097-117379662	GM12878	blood:	n/a	n/a
3	EP300	chr9:117379112-117379680	GM12878	blood:	n/a	chr9:117379213-117379227 chr9:117379207-117379221
4	POLR2A	chr9:117379073-117379668	GM12878	blood:	n/a	n/a
5	ATF2	chr9:117379070-117379664	GM12878	blood:	n/a	n/a
6	ZNF143	chr9:117379514-117379866	K562	blood:	n/a	n/a
7	SPI1	chr9:117379013-117379620	GM12878	blood:	n/a	chr9:117379216-117379229
8	POLR2A	chr9:117379251-117379727	HL-60	blood:	n/a	n/a
9	GATA2	chr9:117379452-117379847	K562	blood:	n/a	chr9:117379660-117379667
10	TCF12	chr9:117379283-117379624	GM12878	blood:	n/a	n/a
11	TCF3	chr9:117379359-117379650	GM12878	blood:	n/a	n/a
12	POLR2A	chr9:117379035-117379895	GM12878	blood:	n/a	n/a
13	TBL1XR1	chr9:117379059-117379743	GM12878	blood:	n/a	n/a
14	TRIM28	chr9:117379386-117379945	K562	blood:	n/a	n/a
15	SPI1	chr9:117378808-117379631	GM12878	blood:	n/a	chr9:117379216-117379229
16	MYC	chr9:117379275-117379861	K562	blood:	n/a	n/a
17	TBL1XR1	chr9:117379578-117379845	K562	blood:	n/a	n/a
18	PAX5	chr9:117379168-117379780	GM12878	blood:	n/a	chr9:117379213-117379222
19	STAT5A	chr9:117378918-117379725	GM12878	blood:	n/a	chr9:117379211-117379222
20	IRF3	chr9:117379454-117379592	GM12878	blood:	n/a	n/a
21	EP300	chr9:117379337-117379671	GM12878	blood:	n/a	n/a
22	EBF1	chr9:117378915-117379743	GM12878	blood:	n/a	chr9:117379231-117379242
23	NR2F2	chr9:117378913-117379877	MCF-7	breast:	n/a	chr9:117379587-117379602
24	TEAD4	chr9:117379356-117379869	K562	blood:	n/a	n/a
25	NFATC1	chr9:117379077-117379680	GM12878	blood:	n/a	n/a
26	POLR2A	chr9:117379380-117379813	K562	blood:	n/a	n/a
27	HCFC1	chr9:117379470-117379786	K562	blood:	n/a	n/a
28	YY1	chr9:117379548-117379807	K562	blood:	n/a	n/a
29	CBX3	chr9:117379289-117379966	K562	blood:	n/a	n/a
30	MAX	chr9:117379284-117379814	K562	blood:	n/a	n/a
31	ZNF384	chr9:117378809-117379761	GM12878	blood:	n/a	n/a
32	POU2F2	chr9:117379126-117379670	GM12878	blood:	n/a	n/a
33	IRF1	chr9:117379072-117379844	K562	blood:	n/a	chr9:117379205-117379219 chr9:117379595-117379605 chr9:117379209-117379223 chr9:117379204-117379224 chr9:117379205-117379218 chr9:117379594-117379605 chr9:117379208-117379222 chr9:117379595-117379609 chr9:117379205-117379216 chr9:117379210-117379221 chr9:117379589-117379606 chr9:117379214-117379223 chr9:117379206-117379220 chr9:117379210-117379224 chr9:117379591-117379605
34	NFATC1	chr9:117379043-117379623	GM12878	blood:	n/a	n/a
35	MTA3	chr9:117379092-117379852	GM12878	blood:	n/a	n/a
36	RUNX3	chr9:117378857-117379837	GM12878	blood:	n/a	n/a
37	SPI1	chr9:117378999-117379611	GM12891	blood:	n/a	chr9:117379216-117379229
38	EBF1	chr9:117378965-117379707	GM12878	blood:	n/a	chr9:117379231-117379242
39	EP300	chr9:117379504-117379869	K562	blood:	n/a	n/a
40	KAP1	chr9:117379188-117379990	K562	blood:	n/a	n/a
41	FOXM1	chr9:117379227-117379876	GM12878	blood:	n/a	n/a
42	TEAD4	chr9:117379442-117379868	K562	blood:	n/a	n/a
43	ZBTB7A	chr9:117379406-117379768	K562	blood:	n/a	n/a
44	SPI1	chr9:117378942-117379762	HL-60	blood:	n/a	chr9:117379216-117379229
45	MAX	chr9:117379234-117379728	GM12878	blood:	n/a	n/a
46	CBX3	chr9:117379475-117379865	K562	blood:	n/a	n/a
47	MAZ	chr9:117379140-117379819	GM12878	blood:	n/a	n/a
48	IKZF1	chr9:117378971-117379628	GM12878	blood:	n/a	n/a
49	ELF1	chr9:117378845-117379681	GM12878	blood:	n/a	n/a
50	YY1	chr9:117379383-117379797	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:117266855..117268743-chr9:117379428..117381102,2	K562	blood:
2	chr9:117264889..117268621-chr9:117379323..117381348,3	MCF-7	breast:
3	chr9:117349294..117352043-chr9:117375229..117380114,4	MCF-7	breast:

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

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs55720568	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs73656157	0.91[AFR][1000 genomes]

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:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117374600-117381200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:117374600-117387800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:117374800-117384000	Weak transcription	NH-A	brain
4	chr9:117374800-117384200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:117374800-117384200	Weak transcription	NHLF	lung
6	chr9:117375000-117384200	Weak transcription	Left Ventricle	heart
7	chr9:117375000-117384200	Weak transcription	Right Atrium	heart
8	chr9:117375000-117384200	Weak transcription	A549	lung
9	chr9:117375000-117384200	Weak transcription	HSMMtube	muscle
10	chr9:117375000-117388800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:117375000-117388800	Weak transcription	Liver	Liver
12	chr9:117375000-117391200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:117375000-117405200	Weak transcription	Psoas Muscle	Psoas
14	chr9:117375000-117410400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr9:117375200-117380200	Weak transcription	Fetal Lung	lung
16	chr9:117375200-117381400	Weak transcription	Osteobl	bone
17	chr9:117375200-117385600	Weak transcription	Fetal Intestine Small	intestine
18	chr9:117375200-117388800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr9:117375200-117388800	Weak transcription	Aorta	Aorta
20	chr9:117375200-117388800	Weak transcription	Pancreas	Pancrea
21	chr9:117375200-117389800	Weak transcription	Fetal Brain Male	brain
22	chr9:117375200-117405400	Weak transcription	Small Intestine	intestine
23	chr9:117375400-117389800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr9:117375600-117388800	Weak transcription	Brain Substantia Nigra	brain
25	chr9:117375600-117389600	Weak transcription	Brain Germinal Matrix	brain
26	chr9:117375600-117405400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr9:117375800-117380400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr9:117375800-117381600	Weak transcription	Colonic Mucosa	Colon
29	chr9:117375800-117381600	Weak transcription	Hela-S3	cervix
30	chr9:117375800-117388800	Weak transcription	Fetal Intestine Large	intestine
31	chr9:117375800-117389800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr9:117375800-117409200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:117375800-117415600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr9:117376000-117381000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr9:117376000-117381200	Weak transcription	NHEK	skin
36	chr9:117376000-117384000	Weak transcription	Fetal Brain Female	brain
37	chr9:117376000-117389000	Weak transcription	Brain Hippocampus Middle	brain
38	chr9:117376200-117381000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr9:117376200-117381200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr9:117376200-117384200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr9:117376200-117388800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr9:117376200-117390000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr9:117376200-117390000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr9:117376200-117415600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr9:117376400-117380600	Weak transcription	Primary T cells from cord blood	blood
46	chr9:117376400-117384000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr9:117376400-117391200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr9:117376400-117396800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr9:117376600-117396200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr9:117377000-117381600	Weak transcription	Ovary	ovary

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