Variant report

Variant	rs28738803
Chromosome Location	chr9:95861492-95861493
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	STAT3	chr9:95861085-95861514	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr9:95860823-95861507	MCF10A-Er-Src	breast:	n/a	chr9:95861044-95861056 chr9:95861045-95861055 chr9:95861027-95861039 chr9:95861029-95861037 chr9:95861045-95861054 chr9:95861044-95861055 chr9:95861027-95861038
3	RCOR1	chr9:95860188-95862102	IMR90	lung:	n/a	n/a
4	FOS	chr9:95860851-95861493	MCF10A-Er-Src	breast:	n/a	chr9:95861044-95861056 chr9:95861045-95861055 chr9:95861027-95861039 chr9:95861029-95861037 chr9:95861045-95861054 chr9:95861044-95861055 chr9:95861027-95861038

No.	Distal block	Cell Line	Cell type
1	chr9:95855712..95863110-chr9:95867626..95874665,14	K562	blood:
2	chr9:95855662..95862507-chr9:95894736..95899302,16	MCF-7	breast:
3	chr9:95857571..95862229-chr9:96211597..96216359,5	K562	blood:
4	chr9:95810158..95812137-chr9:95860234..95862505,2	K562	blood:
5	chr9:95816364..95826268-chr9:95852309..95863275,20	MCF-7	breast:
6	chr9:95765841..95768225-chr9:95860926..95862448,2	MCF-7	breast:
7	chr9:95855064..95861522-chr9:95867449..95872462,10	MCF-7	breast:
8	chr9:95855552..95862102-chr9:95867626..95876894,17	K562	blood:
9	chr9:95856253..95862485-chr9:95892353..95899486,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223446	TF binding region
ENSG00000157303	Chromatin interaction
ENSG00000188938	Chromatin interaction
ENSG00000165233	Chromatin interaction
ENSG00000048828	Chromatin interaction
ENSG00000131669	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10117438	1.00[AMR][1000 genomes]
rs12343422	1.00[AMR][1000 genomes]
rs12348371	1.00[AMR][1000 genomes]
rs12349917	1.00[AMR][1000 genomes]
rs34200537	1.00[AMR][1000 genomes]
rs4077823	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1054767	chr9:95738134-95875977	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv1824329	chr9:95811604-95921347	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv893577	chr9:95812707-95872216	Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv893578	chr9:95818641-95887320	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv893579	chr9:95855100-95923091	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95858800-95861800	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr9:95859000-95861800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
3	chr9:95859000-95862000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr9:95859000-95862800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr9:95859000-95862800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:95859200-95861800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr9:95859200-95861800	Enhancers	K562	blood
8	chr9:95859400-95862200	Enhancers	Pancreas	Pancrea
9	chr9:95859400-95862200	Enhancers	Spleen	Spleen
10	chr9:95859400-95862400	Enhancers	Primary B cells from peripheral blood	blood
11	chr9:95859400-95876200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:95859600-95861600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:95859600-95861800	Enhancers	Liver	Liver
14	chr9:95859600-95861800	Enhancers	Lung	lung
15	chr9:95859600-95861800	Enhancers	Small Intestine	intestine
16	chr9:95859600-95862000	Enhancers	Fetal Lung	lung
17	chr9:95859600-95862200	Enhancers	Gastric	stomach
18	chr9:95859600-95862200	Enhancers	Right Atrium	heart
19	chr9:95859600-95862400	Enhancers	Placenta	Placenta
20	chr9:95859600-95862600	Enhancers	Ovary	ovary
21	chr9:95859600-95889400	Weak transcription	Fetal Kidney	kidney
22	chr9:95859800-95862000	Enhancers	Stomach Mucosa	stomach
23	chr9:95859800-95862200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr9:95859800-95862200	Enhancers	Fetal Muscle Leg	muscle
25	chr9:95859800-95862400	Enhancers	Left Ventricle	heart
26	chr9:95859800-95862600	Enhancers	Esophagus	oesophagus
27	chr9:95860000-95862800	Enhancers	Fetal Thymus	thymus
28	chr9:95860000-95863000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr9:95860200-95861600	Enhancers	Fetal Brain Male	brain
30	chr9:95860200-95862200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:95860200-95872600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:95860400-95861800	Enhancers	Fetal Intestine Large	intestine
33	chr9:95860400-95861800	Enhancers	Fetal Muscle Trunk	muscle
34	chr9:95860400-95862400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:95860400-95862400	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr9:95860400-95863000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:95860400-95876400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr9:95860600-95861600	Enhancers	Fetal Stomach	stomach
39	chr9:95860800-95863000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr9:95860800-95863000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr9:95860800-95872800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr9:95861000-95861600	Enhancers	Primary hematopoietic stem cells	blood
43	chr9:95861000-95861600	Active TSS	Brain Germinal Matrix	brain
44	chr9:95861000-95861600	Weak transcription	Fetal Intestine Small	intestine
45	chr9:95861000-95861800	Enhancers	Brain Anterior Caudate	brain
46	chr9:95861000-95861800	Weak transcription	Psoas Muscle	Psoas
47	chr9:95861000-95861800	Enhancers	HepG2	liver
48	chr9:95861000-95861800	Enhancers	HSMMtube	muscle
49	chr9:95861000-95862000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr9:95861000-95862000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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