Variant report

Variant	rs10981519
Chromosome Location	chr9:115600599-115600600
allele	G/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	chr9:115600581-115600885	GM12891	blood:	n/a	n/a
2	SPI1	chr9:115600558-115600852	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
SNX30	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10117017	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10117709	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10122712	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10481638	0.80[MEX][hapmap]
rs10513168	0.90[CEU][hapmap];0.95[TSI][hapmap]
rs10513169	1.00[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs10732374	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10733595	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10739371	0.89[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs10759587	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10759588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10817391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10817393	0.84[JPT][hapmap]
rs10817394	0.86[JPT][hapmap]
rs10817395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817396	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10981513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981515	0.91[ASN][1000 genomes]
rs10981516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981520	0.84[JPT][hapmap]
rs10981521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981522	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981523	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981530	0.86[EUR][1000 genomes]
rs10981531	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10981532	0.81[EUR][1000 genomes]
rs10981533	0.81[EUR][1000 genomes]
rs11791125	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793016	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418408	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1539345	0.99[ASN][1000 genomes]
rs1573055	0.92[EUR][1000 genomes]
rs1573056	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs16917440	1.00[CEU][hapmap]
rs17742501	1.00[CEU][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs17742994	1.00[CEU][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs17743418	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs17743824	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17821593	1.00[CEU][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs2000204	0.89[ASN][1000 genomes]
rs2096186	0.84[ASN][1000 genomes]
rs2096187	0.80[ASN][1000 genomes]
rs2153839	0.89[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2185767	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796024	0.89[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs41280189	0.96[EUR][1000 genomes]
rs4276760	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4574920	1.00[CEU][hapmap]
rs4978504	0.90[ASN][1000 genomes]
rs4979158	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4979162	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4979163	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4979164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4979166	0.89[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs57546880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57672123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58247585	0.96[EUR][1000 genomes]
rs59645636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60989307	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61626147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62576385	0.85[EUR][1000 genomes]
rs62576386	0.86[EUR][1000 genomes]
rs62576389	0.86[EUR][1000 genomes]
rs62576390	0.86[EUR][1000 genomes]
rs62576391	0.86[EUR][1000 genomes]
rs62576394	0.86[EUR][1000 genomes]
rs62576395	0.86[EUR][1000 genomes]
rs62576396	0.86[EUR][1000 genomes]
rs62576405	0.86[EUR][1000 genomes]
rs62576406	0.86[EUR][1000 genomes]
rs62576407	0.86[EUR][1000 genomes]
rs62576409	0.86[EUR][1000 genomes]
rs62576410	0.86[EUR][1000 genomes]
rs62576411	0.86[EUR][1000 genomes]
rs62576412	0.88[EUR][1000 genomes]
rs62576413	0.93[EUR][1000 genomes]
rs62576414	0.93[EUR][1000 genomes]
rs62576415	0.93[EUR][1000 genomes]
rs62576438	0.86[EUR][1000 genomes]
rs6477960	0.88[ASN][1000 genomes]
rs6477961	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7030460	0.91[ASN][1000 genomes]
rs7032401	0.89[ASN][1000 genomes]
rs7856199	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7871799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs787282	0.87[ASN][1000 genomes]
rs787283	0.88[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs787288	0.89[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs7873644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs870078	0.89[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs883462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299210	0.94[ASN][1000 genomes]
rs999018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10981519	SLC31A2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115565000-115600800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr9:115565600-115600800	Weak transcription	HMEC	breast
3	chr9:115570600-115608400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:115573600-115607800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr9:115575000-115600800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr9:115577600-115630400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr9:115579000-115600800	Weak transcription	Fetal Brain Male	brain
8	chr9:115580200-115608400	Weak transcription	Fetal Kidney	kidney
9	chr9:115580600-115601800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:115582200-115608600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr9:115582400-115600600	Weak transcription	HSMM	muscle
12	chr9:115582400-115608600	Weak transcription	NHLF	lung
13	chr9:115582400-115609000	Weak transcription	NHDF-Ad	bronchial
14	chr9:115582400-115630000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr9:115584400-115608800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:115591200-115606800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr9:115591400-115623200	Weak transcription	Fetal Heart	heart
18	chr9:115592600-115607200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr9:115593200-115611000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr9:115593400-115602600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr9:115593600-115607200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr9:115594000-115602800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:115594200-115600600	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr9:115594200-115600800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:115594200-115603000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr9:115594200-115607200	Weak transcription	Fetal Thymus	thymus
27	chr9:115594200-115610800	Weak transcription	Esophagus	oesophagus
28	chr9:115594200-115616000	Weak transcription	Small Intestine	intestine
29	chr9:115594200-115620400	Weak transcription	Thymus	Thymus
30	chr9:115594200-115634400	Weak transcription	NH-A	brain
31	chr9:115594400-115601400	Weak transcription	Fetal Brain Female	brain
32	chr9:115594400-115608600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr9:115594400-115626800	Weak transcription	Colon Smooth Muscle	Colon
34	chr9:115594600-115607200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr9:115594600-115607200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr9:115595600-115602400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr9:115596200-115604000	Strong transcription	Fetal Stomach	stomach
38	chr9:115596400-115613600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr9:115596600-115601200	Enhancers	Stomach Mucosa	stomach
40	chr9:115597400-115605600	Strong transcription	Primary T cells from cord blood	blood
41	chr9:115597600-115600600	Weak transcription	HSMMtube	muscle
42	chr9:115598000-115605000	Strong transcription	Fetal Muscle Leg	muscle
43	chr9:115598200-115601000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr9:115598200-115602400	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr9:115598200-115602600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:115598400-115601000	Strong transcription	Aorta	Aorta
47	chr9:115598400-115601400	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr9:115598400-115602400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr9:115598400-115602600	Strong transcription	Ovary	ovary
50	chr9:115598400-115602800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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