Variant report

Variant	rs28560439
Chromosome Location	chr8:9911034-9911035
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	POLR2A	chr8:9910959-9913289	GM12878	blood:	n/a	n/a
2	POLR2A	chr8:9910902-9913264	GM12891	blood:	n/a	n/a
3	POLR2A	chr8:9910893-9911883	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr8:9910961-9911137	HepG2	liver:	n/a	n/a
5	MXI1	chr8:9910994-9913437	SK-N-SH	brain:	n/a	chr8:9911023-9911038
6	MXI1	chr8:9910720-9912976	IMR90	lung:	n/a	chr8:9911023-9911038

Variant related genes	Relation type
MSRA	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10081447	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10101206	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10109617	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11985392	0.83[AFR][1000 genomes]
rs11985767	0.87[ASN][1000 genomes]
rs2293090	1.00[ASN][1000 genomes]
rs6995352	0.87[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	nsv530864	chr8:9097498-9914548	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv916493	chr8:9806580-10029482	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv869934	chr8:9806639-9940586	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv890343	chr8:9888729-9932797	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv971581	chr8:9910302-9911256	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9906200-9911200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:9907000-9911200	Weak transcription	Brain Hippocampus Middle	brain
3	chr8:9909000-9911200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr8:9910800-9911200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr8:9910800-9911200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr8:9910800-9911200	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr8:9910800-9911200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr8:9910800-9911200	Enhancers	Brain Angular Gyrus	brain
9	chr8:9910800-9911200	Enhancers	Fetal Heart	heart
10	chr8:9910800-9911200	Enhancers	Fetal Intestine Small	intestine
11	chr8:9910800-9911200	Enhancers	Fetal Kidney	kidney
12	chr8:9910800-9911200	Enhancers	Fetal Lung	lung
13	chr8:9910800-9911200	Enhancers	Fetal Thymus	thymus
14	chr8:9910800-9911400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr8:9910800-9911400	Enhancers	Primary T cells fromperipheralblood	blood
16	chr8:9910800-9911400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr8:9910800-9911600	Flanking Active TSS	Liver	Liver
18	chr8:9910800-9911600	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr8:9910800-9912800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr8:9911000-9911200	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr8:9911000-9911200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr8:9911000-9911200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr8:9911000-9911200	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr8:9911000-9911200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr8:9911000-9911200	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr8:9911000-9911200	Enhancers	Primary hematopoietic stem cells	blood
27	chr8:9911000-9911200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr8:9911000-9911200	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr8:9911000-9911200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr8:9911000-9911200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr8:9911000-9911200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr8:9911000-9911200	Enhancers	Muscle Satellite Cultured Cells	--
33	chr8:9911000-9911200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr8:9911000-9911200	Flanking Active TSS	Brain Germinal Matrix	brain
35	chr8:9911000-9911200	Enhancers	Brain Substantia Nigra	brain
36	chr8:9911000-9911200	Enhancers	Colon Smooth Muscle	Colon
37	chr8:9911000-9911200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr8:9911000-9911200	Enhancers	Fetal Intestine Large	intestine
39	chr8:9911000-9911200	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr8:9911000-9911200	Enhancers	Fetal Muscle Leg	muscle
41	chr8:9911000-9911200	Enhancers	Pancreas	Pancrea
42	chr8:9911000-9911200	Enhancers	Psoas Muscle	Psoas
43	chr8:9911000-9911200	Enhancers	Right Atrium	heart
44	chr8:9911000-9911200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr8:9911000-9911200	Enhancers	Stomach Mucosa	stomach
46	chr8:9911000-9911200	Flanking Active TSS	HepG2	liver
47	chr8:9911000-9911200	Enhancers	NHLF	lung
48	chr8:9911000-9911400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr8:9911000-9911400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr8:9911000-9911400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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