Variant report

Variant	rs483284
Chromosome Location	chr9:116379646-116379647
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	EP300	chr9:116379409-116380482	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr9:116379646-116380373	SK-N-SH	brain:	n/a	n/a
3	EBF1	chr9:116379415-116379797	GM12878	blood:	n/a	chr9:116379605-116379616
4	EBF1	chr9:116379473-116379742	GM12878	blood:	n/a	chr9:116379605-116379616
5	EBF1	chr9:116379516-116379722	GM12878	blood:	n/a	chr9:116379605-116379616
6	POLR2A	chr9:116379548-116379648	H1-hESC	embryonic stem cell:	n/a	n/a
7	ELF1	chr9:116379411-116379757	GM12878	blood:	n/a	n/a
8	RELA	chr9:116379518-116379893	GM18951	blood:	n/a	chr9:116379703-116379712 chr9:116379703-116379712
9	RELA	chr9:116379478-116379974	GM19193	blood:	n/a	chr9:116379703-116379712 chr9:116379703-116379712
10	RELA	chr9:116379470-116380158	GM12891	blood:	n/a	chr9:116379703-116379712 chr9:116379703-116379712

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:116376834..116379828-chr9:116381468..116382973,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233817	TF binding region
ENSG00000233817	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1547694	0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs2039225	0.87[EUR][1000 genomes]
rs2812400	0.91[AFR][1000 genomes]
rs485184	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs502942	0.91[AFR][1000 genomes]
rs505668	0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs530456	1.00[CEU][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs538711	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs551960	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs565016	0.87[EUR][1000 genomes]
rs586265	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs608290	1.00[CEU][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs611335	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs641266	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs653971	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs664850	0.94[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs670719	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893747	chr9:116214058-116386438	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS 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	13 gene(s)	inside rSNPs	diseases
3	nsv526579	chr9:116244982-116391162	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv893748	chr9:116308709-116421786	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS 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	13 gene(s)	inside rSNPs	diseases
5	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
6	nsv466509	chr9:116356516-116396098	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription 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 target site	8 gene(s)	inside rSNPs	diseases
7	nsv615216	chr9:116356516-116396098	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv466510	chr9:116363877-116397397	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv615217	chr9:116363877-116397397	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv615218	chr9:116365126-116391069	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv466511	chr9:116374990-116397397	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv615219	chr9:116374990-116397397	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv893749	chr9:116378759-116439749	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116371200-116380200	Enhancers	Fetal Muscle Leg	muscle
2	chr9:116373600-116379800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:116373600-116382400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:116373800-116380000	Enhancers	Spleen	Spleen
5	chr9:116375200-116379800	Enhancers	Right Ventricle	heart
6	chr9:116375600-116382400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr9:116376200-116379800	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr9:116376200-116380000	Enhancers	Ovary	ovary
9	chr9:116376200-116380200	Enhancers	Fetal Stomach	stomach
10	chr9:116376200-116386000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr9:116376400-116380200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:116376800-116379800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr9:116376800-116380000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:116376800-116382200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr9:116377000-116382200	Enhancers	Primary B cells from cord blood	blood
16	chr9:116377000-116382800	Enhancers	Primary B cells from peripheral blood	blood
17	chr9:116377400-116380200	Enhancers	Fetal Lung	lung
18	chr9:116377400-116381600	Weak transcription	Brain Germinal Matrix	brain
19	chr9:116377400-116382200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr9:116377400-116382400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:116377800-116380000	Enhancers	HSMMtube	muscle
22	chr9:116377800-116380200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr9:116377800-116381200	Weak transcription	Fetal Kidney	kidney
24	chr9:116377800-116381600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr9:116377800-116382200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:116377800-116382200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr9:116377800-116382400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:116378000-116381200	Weak transcription	Stomach Mucosa	stomach
29	chr9:116378000-116381400	Weak transcription	Gastric	stomach
30	chr9:116378000-116381400	Weak transcription	Pancreas	Pancrea
31	chr9:116378000-116381600	Weak transcription	Colon Smooth Muscle	Colon
32	chr9:116378000-116381600	Weak transcription	Fetal Intestine Small	intestine
33	chr9:116378000-116381800	Weak transcription	Colonic Mucosa	Colon
34	chr9:116378000-116382400	Weak transcription	Brain Angular Gyrus	brain
35	chr9:116378200-116379800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:116378200-116379800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr9:116378200-116379800	Weak transcription	HSMM	muscle
38	chr9:116378200-116379800	Weak transcription	NH-A	brain
39	chr9:116378200-116380200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:116378200-116382200	Weak transcription	Brain Hippocampus Middle	brain
41	chr9:116378400-116379800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
42	chr9:116378400-116380200	Enhancers	NHDF-Ad	bronchial
43	chr9:116378400-116380600	Enhancers	Stomach Smooth Muscle	stomach
44	chr9:116378600-116380200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr9:116378600-116382000	Weak transcription	Brain Anterior Caudate	brain
46	chr9:116378600-116382000	Weak transcription	Fetal Intestine Large	intestine
47	chr9:116378600-116382200	Weak transcription	Aorta	Aorta
48	chr9:116378600-116382600	Weak transcription	Psoas Muscle	Psoas
49	chr9:116378800-116380200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:116378800-116382400	Weak transcription	Esophagus	oesophagus

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