Variant report

Variant	rs6479598
Chromosome Location	chr9:97849927-97849928
allele	C/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	TCF12	chr9:97849738-97850518	ECC-1	luminal epithelium:	n/a	n/a
2	BCL3	chr9:97849652-97856909	A549	lung:	n/a	chr9:97849910-97849923 chr9:97856480-97856489 chr9:97852058-97852071
3	BCL3	chr9:97849737-97850530	A549	lung:	n/a	chr9:97849910-97849923
4	RAD21	chr9:97849856-97850419	ECC-1	luminal epithelium:	n/a	chr9:97850180-97850192 chr9:97850178-97850191 chr9:97850175-97850194 chr9:97850180-97850190
5	TCF12	chr9:97849698-97856389	A549	lung:	n/a	chr9:97854161-97854171 chr9:97855868-97855877 chr9:97853824-97853834
6	TCF12	chr9:97849783-97850425	ECC-1	luminal epithelium:	n/a	n/a
7	NFIC	chr9:97849697-97850613	ECC-1	luminal epithelium:	n/a	chr9:97850110-97850127
8	MAX	chr9:97849847-97850548	ECC-1	luminal epithelium:	n/a	chr9:97849915-97849924
9	JUND	chr9:97849856-97850403	A549	lung:	n/a	chr9:97850136-97850143
10	POLR2A	chr9:97849710-97856872	A549	lung:	n/a	n/a
11	CTCF	chr9:97849920-97850070	A549	lung:	n/a	n/a
12	POLR2A	chr9:97849770-97850466	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr9:97849852-97850456	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr9:97849857-97850404	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr9:97849834-97850406	HepG2	liver:	n/a	n/a
16	POLR2A	chr9:97849778-97850317	ECC-1	luminal epithelium:	n/a	n/a
17	NFIC	chr9:97849781-97850482	ECC-1	luminal epithelium:	n/a	chr9:97850110-97850127
18	POLR2A	chr9:97849763-97850022	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr9:97849873-97850535	HepG2	liver:	n/a	n/a
20	MAX	chr9:97849904-97850574	ECC-1	luminal epithelium:	n/a	chr9:97849915-97849924
21	EP300	chr9:97849778-97850509	ECC-1	luminal epithelium:	n/a	n/a
22	CTCF	chr9:97849773-97850517	A549	lung:	n/a	chr9:97850174-97850192 chr9:97850429-97850442 chr9:97850177-97850190
23	CTCF	chr9:97849917-97850434	MCF-7	breast:	n/a	chr9:97850174-97850192 chr9:97850177-97850190

No.	Distal block	Cell Line	Cell type
1	chr9:97542830..97545595-chr9:97848570..97851188,3	MCF-7	breast:
2	chr9:97848613..97851879-chr9:97854740..97857228,3	K562	blood:
3	chr9:97849794..97850649-chr9:97889635..97890557,2	MCF-7	breast:
4	chr9:97688794..97691032-chr9:97848721..97850468,2	MCF-7	breast:
5	chr9:97763635..97773461-chr9:97847821..97861280,36	MCF-7	breast:

Variant related genes	Relation type
MIR3074	TF binding region
ENSG00000148120	Chromatin interaction
ENSG00000158169	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1011784	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10761374	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10821447	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4657	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4743988	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4744442	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7042293	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7042320	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7046682	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7874388	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
5	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97813000-97873000	Weak transcription	K562	blood
2	chr9:97820000-97854200	Weak transcription	Fetal Brain Male	brain
3	chr9:97820600-97875000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr9:97825400-97854400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr9:97825800-97852600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr9:97838000-97871200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr9:97839600-97850400	Strong transcription	HepG2	liver
8	chr9:97839600-97851000	Genic enhancers	A549	lung
9	chr9:97840000-97850000	Strong transcription	Osteobl	bone
10	chr9:97840800-97851800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr9:97841200-97864400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:97841400-97853000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:97841600-97850000	Strong transcription	NHLF	lung
14	chr9:97841600-97855000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:97841800-97851600	Strong transcription	Fetal Intestine Small	intestine
16	chr9:97841800-97853800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr9:97841800-97854000	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr9:97842200-97850600	Strong transcription	Fetal Lung	lung
19	chr9:97842200-97852000	Strong transcription	NHEK	skin
20	chr9:97842400-97850000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:97842400-97850200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:97842400-97852600	Strong transcription	Fetal Intestine Large	intestine
23	chr9:97842400-97854200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr9:97842800-97850800	Strong transcription	Placenta	Placenta
25	chr9:97843000-97850200	Strong transcription	Adipose Nuclei	Adipose
26	chr9:97843200-97851600	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr9:97843200-97851800	Genic enhancers	Brain Hippocampus Middle	brain
28	chr9:97843200-97852400	Genic enhancers	Rectal Smooth Muscle	rectum
29	chr9:97843600-97850200	Strong transcription	Ovary	ovary
30	chr9:97843600-97853400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:97844000-97854800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr9:97844000-97898400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr9:97844400-97852200	Strong transcription	Fetal Stomach	stomach
34	chr9:97844400-97854200	Weak transcription	Brain Germinal Matrix	brain
35	chr9:97845000-97852600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr9:97845400-97850200	Weak transcription	Fetal Thymus	thymus
37	chr9:97845800-97854400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr9:97845800-97854400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr9:97846000-97850000	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr9:97846000-97850800	Weak transcription	Right Atrium	heart
41	chr9:97846000-97853000	Weak transcription	Fetal Kidney	kidney
42	chr9:97846000-97853200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr9:97846000-97853800	Weak transcription	GM12878-XiMat	blood
44	chr9:97846000-97861600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr9:97846200-97851200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr9:97846200-97853400	Weak transcription	Small Intestine	intestine
47	chr9:97846200-97853600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr9:97846200-97880000	Weak transcription	Primary B cells from cord blood	blood
49	chr9:97846800-97850000	Strong transcription	Lung	lung
50	chr9:97847000-97852600	Genic enhancers	Colon Smooth Muscle	Colon

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