Variant report

Variant	rs4979443
Chromosome Location	chr9:117375554-117375555
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	POLR2A	chr9:117372694-117376306	GM12878	blood:	n/a	n/a
2	CEBPB	chr9:117375460-117375660	Hela-S3	cervix:	n/a	chr9:117375556-117375567 chr9:117375557-117375568 chr9:117375556-117375569
3	MTA3	chr9:117373827-117376338	GM12878	blood:	n/a	n/a
4	GATA3	chr9:117374385-117375621	T-47D	breast:	n/a	n/a
5	NFIC	chr9:117375032-117375960	GM12878	blood:	n/a	n/a
6	CUX1	chr9:117375039-117375811	GM12878	blood:	n/a	chr9:117375796-117375810
7	POLR2A	chr9:117372690-117375775	GM12878	blood:	n/a	n/a
8	MTA3	chr9:117375038-117376004	GM12878	blood:	n/a	n/a
9	FOXM1	chr9:117374667-117375651	GM12878	blood:	n/a	n/a
10	CEBPB	chr9:117375472-117375663	HepG2	liver:	n/a	chr9:117375556-117375567 chr9:117375557-117375568 chr9:117375556-117375569
11	RUNX3	chr9:117375202-117375744	GM12878	blood:	n/a	n/a
12	POLR2A	chr9:117375536-117375722	MCF10A-Er-Src	breast:	n/a	n/a
13	EP300	chr9:117375359-117375740	GM12878	blood:	n/a	chr9:117375554-117375568
14	RUNX3	chr9:117374797-117375984	GM12878	blood:	n/a	n/a
15	ZEB1	chr9:117375286-117375869	GM12878	blood:	n/a	n/a
16	POLR2A	chr9:117372573-117376345	GM12878	blood:	n/a	n/a
17	SMC3	chr9:117375170-117375655	GM12878	blood:	n/a	n/a
18	CHD1	chr9:117374921-117376023	GM12878	blood:	n/a	n/a
19	WRNIP1	chr9:117374148-117377038	GM12878	blood:	n/a	n/a
20	GATA3	chr9:117375253-117375835	T-47D	breast:	n/a	n/a
21	MAX	chr9:117372765-117375754	GM12878	blood:	n/a	chr9:117373514-117373521 chr9:117373512-117373522 chr9:117373568-117373577 chr9:117373513-117373523 chr9:117373513-117373522 chr9:117373512-117373523 chr9:117373514-117373523 chr9:117373511-117373524
22	BHLHE40	chr9:117375191-117375752	GM12878	blood:	n/a	n/a
23	POLR2A	chr9:117372721-117376079	GM12891	blood:	n/a	n/a
24	STAT3	chr9:117375150-117375582	GM12878	blood:	n/a	n/a
25	EP300	chr9:117374957-117375956	GM12878	blood:	n/a	chr9:117375554-117375568
26	EBF1	chr9:117375308-117376195	GM12878	blood:	n/a	n/a
27	STAT1	chr9:117374853-117375620	GM12878	blood:	n/a	n/a
28	POLR2A	chr9:117372060-117376570	GM12878	blood:	n/a	n/a
29	BCL3	chr9:117375321-117375712	GM12878	blood:	n/a	n/a
30	EBF1	chr9:117375375-117375787	GM12878	blood:	n/a	n/a
31	FOXM1	chr9:117374885-117375837	GM12878	blood:	n/a	n/a
32	MAZ	chr9:117375373-117375781	GM12878	blood:	n/a	n/a
33	USF2	chr9:117375309-117375613	GM12878	blood:	n/a	n/a
34	RCOR1	chr9:117374932-117375729	GM12878	blood:	n/a	n/a
35	ZNF143	chr9:117374828-117375660	GM12878	blood:	n/a	n/a
36	PML	chr9:117374928-117375949	GM12878	blood:	n/a	n/a
37	POLR2A	chr9:117373828-117376507	GM12878	blood:	n/a	n/a
38	CEBPB	chr9:117375436-117375761	K562	blood:	n/a	chr9:117375556-117375567 chr9:117375557-117375568 chr9:117375556-117375569
39	MXI1	chr9:117373033-117376008	GM12878	blood:	n/a	n/a
40	CTCF	chr9:117375420-117375570	MCF-7	breast:	n/a	n/a
41	NFATC1	chr9:117375031-117375811	GM12878	blood:	n/a	n/a
42	CEBPB	chr9:117375002-117375906	GM12878	blood:	n/a	chr9:117375556-117375567 chr9:117375557-117375568 chr9:117375556-117375569
43	TBP	chr9:117375134-117375965	GM12878	blood:	n/a	n/a
44	TBL1XR1	chr9:117374960-117376024	GM12878	blood:	n/a	n/a
45	CHD2	chr9:117374853-117375995	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:117373836..117375707-chr9:117400853..117402924,2	MCF-7	breast:
2	chr9:117291759..117293963-chr9:117373811..117375856,2	K562	blood:
3	chr9:117374384..117377233-chr9:117400977..117403274,2	K562	blood:
4	chr9:117349294..117352043-chr9:117375229..117380114,4	MCF-7	breast:
5	chr9:117348104..117352194-chr9:117371141..117379325,14	K562	blood:
6	chr9:117346757..117362857-chr9:117372020..117377914,21	MCF-7	breast:
7	chr9:117262731..117268447-chr9:117369704..117378306,14	K562	blood:
8	chr9:117266234..117268906-chr9:117372659..117377270,6	K562	blood:
9	chr9:117301959..117303545-chr9:117375054..117376572,2	MCF-7	breast:
10	chr9:117248554..117250072-chr9:117374914..117376570,2	MCF-7	breast:
11	chr9:117263907..117271703-chr9:117371218..117376768,10	MCF-7	breast:
12	chr9:117250118..117252252-chr9:117374718..117376331,2	MCF-7	breast:
13	chr9:117372326..117374917-chr9:117375396..117377851,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATP6V1G1-2	chr9:117374792-117377101	NONHSAT134388

Variant related genes	Relation type
ENSG00000272241	TF binding region
ENSG00000095397	Chromatin interaction
ENSG00000157693	Chromatin interaction
ENSG00000136888	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10982331	0.96[ASN][1000 genomes]
rs10982332	0.92[ASN][1000 genomes]
rs12343284	0.81[JPT][hapmap]
rs1887785	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2149372	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2418309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7019176	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4979443	C9orf91	cis	lymphoblastoid	seeQTL
rs4979443	ATP6V1G1	Cis_1M	lymphoblastoid	RTeQTL
rs4979443	C9orf91	Cis_1M	lymphoblastoid	RTeQTL
rs4979443	Contig10670_RC	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117374000-117376000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr9:117374000-117376200	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr9:117374400-117375800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr9:117374400-117376000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:117374400-117376400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:117374400-117377000	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr9:117374600-117375800	Weak transcription	Fetal Kidney	kidney
8	chr9:117374600-117376000	Flanking Active TSS	Dnd41	blood
9	chr9:117374600-117376200	Enhancers	H1 Cell Line	embryonic stem cell
10	chr9:117374600-117376200	Enhancers	Placenta Amnion	Placenta Amnion
11	chr9:117374600-117376200	Flanking Active TSS	GM12878-XiMat	blood
12	chr9:117374600-117381200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:117374600-117387800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr9:117374800-117375600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr9:117374800-117375600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:117374800-117375600	Enhancers	Brain Substantia Nigra	brain
17	chr9:117374800-117375800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr9:117374800-117375800	Enhancers	Fetal Intestine Large	intestine
19	chr9:117374800-117375800	Enhancers	Fetal Stomach	stomach
20	chr9:117374800-117375800	Enhancers	Lung	lung
21	chr9:117374800-117375800	Enhancers	Stomach Mucosa	stomach
22	chr9:117374800-117376000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr9:117374800-117376000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr9:117374800-117376000	Enhancers	Spleen	Spleen
25	chr9:117374800-117376000	Enhancers	NHEK	skin
26	chr9:117374800-117376200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr9:117374800-117376200	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr9:117374800-117376200	Enhancers	Fetal Thymus	thymus
29	chr9:117374800-117376600	Enhancers	H9 Cell Line	embryonic stem cell
30	chr9:117374800-117377000	Enhancers	Placenta	Placenta
31	chr9:117374800-117377000	Enhancers	Ovary	ovary
32	chr9:117374800-117384000	Weak transcription	NH-A	brain
33	chr9:117374800-117384200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:117374800-117384200	Weak transcription	NHLF	lung
35	chr9:117375000-117375600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:117375000-117375600	Enhancers	Brain Germinal Matrix	brain
37	chr9:117375000-117375800	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr9:117375000-117375800	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr9:117375000-117376000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:117375000-117376000	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr9:117375000-117376000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr9:117375000-117376000	Enhancers	Brain Hippocampus Middle	brain
43	chr9:117375000-117376000	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr9:117375000-117376000	Enhancers	K562	blood
45	chr9:117375000-117376200	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr9:117375000-117376200	Enhancers	Primary hematopoietic stem cells	blood
47	chr9:117375000-117376200	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr9:117375000-117376200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr9:117375000-117376200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr9:117375000-117376400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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