Variant report

Variant	rs10513169
Chromosome Location	chr9:115593870-115593871
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10513168	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs10817391	0.93[EUR][1000 genomes]
rs10817392	0.93[EUR][1000 genomes]
rs10817395	0.93[EUR][1000 genomes]
rs10981493	0.86[ASN][1000 genomes]
rs10981513	1.00[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs10981516	0.93[EUR][1000 genomes]
rs10981519	1.00[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs10981521	0.93[EUR][1000 genomes]
rs10981522	0.93[EUR][1000 genomes]
rs10981523	1.00[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs10981530	0.87[EUR][1000 genomes]
rs10981531	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10981533	0.82[EUR][1000 genomes]
rs11791125	0.93[EUR][1000 genomes]
rs11793016	0.93[EUR][1000 genomes]
rs1573055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16917440	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs17742501	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17742994	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17743418	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17743824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17821593	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[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185767	1.00[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2645988	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs2900558	1.00[AFR][1000 genomes]
rs41280185	1.00[AFR][1000 genomes]
rs41280189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4276760	1.00[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs4574920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57546880	0.93[EUR][1000 genomes]
rs57672123	0.93[EUR][1000 genomes]
rs58247585	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59645636	0.93[EUR][1000 genomes]
rs60989307	0.93[EUR][1000 genomes]
rs61626147	0.93[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];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576366	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576369	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576370	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576371	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576383	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576384	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62576385	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576386	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576389	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576390	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576391	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576392	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576393	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62576407	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576409	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576412	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576438	0.87[EUR][1000 genomes]
rs7467129	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs786963	1.00[CHB][hapmap]
rs883462	1.00[CEU][hapmap];0.96[EUR][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	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	nsv515899	chr9:115359049-115593870	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv2757350	chr9:115371397-115594108	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers 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	15 gene(s)	inside rSNPs	diseases
5	nsv1038306	chr9:115379305-115595695	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv540194	chr9:115379305-115595695	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv430090	chr9:115383445-115594445	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	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
9	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
rs10513169	SLC31A2	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115555800-115597400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr9:115559400-115598400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:115565000-115600800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr9:115565600-115600800	Weak transcription	HMEC	breast
5	chr9:115566800-115598000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr9:115570600-115608400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr9:115573200-115598400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr9:115573400-115595600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr9:115573400-115598800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:115573600-115598400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:115573600-115607800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr9:115574000-115598600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:115575000-115600800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr9:115577600-115630400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr9:115577800-115594000	Weak transcription	NH-A	brain
16	chr9:115578800-115596200	Weak transcription	Gastric	stomach
17	chr9:115579000-115600800	Weak transcription	Fetal Brain Male	brain
18	chr9:115580200-115608400	Weak transcription	Fetal Kidney	kidney
19	chr9:115580600-115601800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr9:115580800-115596400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:115581200-115598600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr9:115581200-115599200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr9:115582200-115608600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr9:115582400-115598200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr9:115582400-115598400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr9:115582400-115600600	Weak transcription	HSMM	muscle
27	chr9:115582400-115608600	Weak transcription	NHLF	lung
28	chr9:115582400-115609000	Weak transcription	NHDF-Ad	bronchial
29	chr9:115582400-115630000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr9:115582600-115594200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr9:115582600-115598600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr9:115583400-115598200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr9:115583400-115598200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:115583600-115598400	Weak transcription	NHEK	skin
35	chr9:115584400-115608800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:115585000-115596000	Weak transcription	Brain Angular Gyrus	brain
37	chr9:115585200-115594200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr9:115586400-115598000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr9:115587000-115598200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr9:115587200-115598600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr9:115591200-115606800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr9:115591400-115623200	Weak transcription	Fetal Heart	heart
43	chr9:115592400-115600000	Weak transcription	Dnd41	blood
44	chr9:115592600-115607200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr9:115593000-115594200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
46	chr9:115593000-115594800	Enhancers	Stomach Mucosa	stomach
47	chr9:115593000-115596400	Strong transcription	Fetal Intestine Large	intestine
48	chr9:115593200-115594000	Enhancers	Primary B cells from peripheral blood	blood
49	chr9:115593200-115594200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr9:115593200-115594200	Strong transcription	Fetal Intestine Small	intestine

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