Variant report

Variant	rs41280189
Chromosome Location	chr9:115600827-115600828
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	SPI1	chr9:115600611-115600892	GM12878	blood:	n/a	n/a
2	SPI1	chr9:115600581-115600885	GM12891	blood:	n/a	n/a
3	SPI1	chr9:115600558-115600852	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
SNX30	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10513169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817391	0.96[EUR][1000 genomes]
rs10817392	0.96[EUR][1000 genomes]
rs10817395	0.96[EUR][1000 genomes]
rs10981493	0.86[ASN][1000 genomes]
rs10981513	0.88[EUR][1000 genomes]
rs10981516	0.96[EUR][1000 genomes]
rs10981519	0.96[EUR][1000 genomes]
rs10981521	0.96[EUR][1000 genomes]
rs10981522	0.96[EUR][1000 genomes]
rs10981523	0.96[EUR][1000 genomes]
rs10981530	0.89[EUR][1000 genomes]
rs10981531	0.89[EUR][1000 genomes]
rs10981533	0.84[EUR][1000 genomes]
rs11791125	0.96[EUR][1000 genomes]
rs11793016	0.96[EUR][1000 genomes]
rs1573055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17742501	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17742994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17743418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17743824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17821593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185767	0.94[EUR][1000 genomes]
rs2645988	0.93[ASN][1000 genomes]
rs2900558	1.00[AFR][1000 genomes]
rs41280185	1.00[AFR][1000 genomes]
rs4276760	0.94[EUR][1000 genomes]
rs4574920	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57546880	0.96[EUR][1000 genomes]
rs57672123	0.96[EUR][1000 genomes]
rs58247585	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59645636	0.96[EUR][1000 genomes]
rs60989307	0.96[EUR][1000 genomes]
rs61626147	0.96[EUR][1000 genomes]
rs62575254	1.00[AFR][1000 genomes]
rs62575257	1.00[AFR][1000 genomes]
rs62576360	1.00[AFR][1000 genomes]
rs62576361	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs62576362	0.84[ASN][1000 genomes]
rs62576365	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576366	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576369	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576370	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576371	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576383	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576384	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576385	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576386	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576389	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576390	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576391	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576392	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576393	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576407	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576409	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576412	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576438	0.89[EUR][1000 genomes]
rs7467129	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs883462	0.93[EUR][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	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv893733	chr9:115397206-115712068	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv2422302	chr9:115550339-115656433	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv2757351	chr9:115600623-115632898	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115570600-115608400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:115573600-115607800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr9:115577600-115630400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr9:115580200-115608400	Weak transcription	Fetal Kidney	kidney
5	chr9:115580600-115601800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:115582200-115608600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:115582400-115608600	Weak transcription	NHLF	lung
8	chr9:115582400-115609000	Weak transcription	NHDF-Ad	bronchial
9	chr9:115582400-115630000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr9:115584400-115608800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:115591200-115606800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr9:115591400-115623200	Weak transcription	Fetal Heart	heart
13	chr9:115592600-115607200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr9:115593200-115611000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr9:115593400-115602600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:115593600-115607200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr9:115594000-115602800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:115594200-115603000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr9:115594200-115607200	Weak transcription	Fetal Thymus	thymus
20	chr9:115594200-115610800	Weak transcription	Esophagus	oesophagus
21	chr9:115594200-115616000	Weak transcription	Small Intestine	intestine
22	chr9:115594200-115620400	Weak transcription	Thymus	Thymus
23	chr9:115594200-115634400	Weak transcription	NH-A	brain
24	chr9:115594400-115601400	Weak transcription	Fetal Brain Female	brain
25	chr9:115594400-115608600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:115594400-115626800	Weak transcription	Colon Smooth Muscle	Colon
27	chr9:115594600-115607200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr9:115594600-115607200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr9:115595600-115602400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:115596200-115604000	Strong transcription	Fetal Stomach	stomach
31	chr9:115596400-115613600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr9:115596600-115601200	Enhancers	Stomach Mucosa	stomach
33	chr9:115597400-115605600	Strong transcription	Primary T cells from cord blood	blood
34	chr9:115598000-115605000	Strong transcription	Fetal Muscle Leg	muscle
35	chr9:115598200-115601000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr9:115598200-115602400	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr9:115598200-115602600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr9:115598400-115601000	Strong transcription	Aorta	Aorta
39	chr9:115598400-115601400	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:115598400-115602400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:115598400-115602600	Strong transcription	Ovary	ovary
42	chr9:115598400-115602800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr9:115598400-115603400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:115598400-115604800	Strong transcription	Fetal Muscle Trunk	muscle
45	chr9:115598600-115601200	Strong transcription	Brain Hippocampus Middle	brain
46	chr9:115598600-115602000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr9:115598600-115602600	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr9:115598600-115602600	Strong transcription	Osteobl	bone
49	chr9:115598600-115615200	Weak transcription	Psoas Muscle	Psoas
50	chr9:115598800-115608400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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