Variant report

Variant	rs10759598
Chromosome Location	chr9:115615580-115615581
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:115607502..115609208-chr9:115615429..115617354,2	MCF-7	breast:
2	chr9:115612240..115614238-chr9:115614501..115616948,2	K562	blood:
3	chr9:115614764..115617679-chr9:115622672..115625535,2	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10115576	0.81[GIH][hapmap];0.83[LWK][hapmap]
rs10117017	0.93[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10117709	0.93[CEU][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10122712	0.93[CEU][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10124939	0.81[GIH][hapmap]
rs10481638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10481671	0.87[CEU][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs10732374	0.93[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10733595	0.93[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10733596	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10733597	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739371	0.93[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs10739375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759587	0.93[CEU][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10759588	0.93[CEU][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10759589	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10759591	0.90[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10759595	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10759596	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10759600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817396	1.00[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10817397	1.00[CEU][hapmap];1.00[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]
rs10817398	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10817399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10817400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10817401	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817402	0.87[CEU][hapmap]
rs10981515	0.81[EUR][1000 genomes]
rs1418408	0.93[CEU][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1475292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1475293	0.81[GIH][hapmap]
rs1539340	1.00[CEU][hapmap];1.00[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]
rs1539341	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1539342	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];0.97[MKK][hapmap];1.00[TSI][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]
rs1539345	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1891403	0.81[GIH][hapmap]
rs1970527	1.00[CEU][hapmap];1.00[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]
rs1970528	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2000204	0.84[EUR][1000 genomes]
rs2645988	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs2676622	0.88[MEX][hapmap]
rs2796024	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs4366151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4367629	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4978511	0.81[GIH][hapmap]
rs4979158	0.93[CEU][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4979162	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4979163	0.93[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4979164	0.93[CEU][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4979166	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4979167	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477961	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7030460	0.84[EUR][1000 genomes]
rs7032763	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs7856199	0.93[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7871799	0.93[CEU][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs787271	0.81[GIH][hapmap]
rs787274	0.81[GIH][hapmap]
rs787280	0.81[GIH][hapmap]
rs787282	0.84[EUR][1000 genomes]
rs787283	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs787288	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs787295	0.81[GIH][hapmap]
rs787297	0.81[GIH][hapmap]
rs7873644	0.93[CEU][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs870078	0.84[EUR][1000 genomes]
rs912661	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299210	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9299211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999018	0.93[CEU][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv1047000	chr9:115610445-115884038	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10759598	TXNDC8	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115577600-115630400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr9:115582400-115630000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr9:115591400-115623200	Weak transcription	Fetal Heart	heart
4	chr9:115594200-115616000	Weak transcription	Small Intestine	intestine
5	chr9:115594200-115620400	Weak transcription	Thymus	Thymus
6	chr9:115594200-115634400	Weak transcription	NH-A	brain
7	chr9:115594400-115626800	Weak transcription	Colon Smooth Muscle	Colon
8	chr9:115599000-115623200	Weak transcription	Right Ventricle	heart
9	chr9:115599400-115623600	Weak transcription	Right Atrium	heart
10	chr9:115599400-115625200	Weak transcription	Colonic Mucosa	Colon
11	chr9:115601200-115641200	Weak transcription	Fetal Brain Male	brain
12	chr9:115601600-115620600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:115602000-115620600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:115602600-115626600	Weak transcription	Brain Germinal Matrix	brain
15	chr9:115602600-115626800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr9:115604000-115626600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr9:115604200-115621200	Weak transcription	HepG2	liver
18	chr9:115607400-115643400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:115607600-115620800	Strong transcription	Fetal Intestine Small	intestine
20	chr9:115607600-115630200	Weak transcription	NHEK	skin
21	chr9:115608600-115617000	Strong transcription	Fetal Intestine Large	intestine
22	chr9:115609400-115623200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr9:115610400-115615600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:115611400-115628600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr9:115611400-115634600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:115611600-115616800	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr9:115611600-115619000	Weak transcription	Fetal Lung	lung
28	chr9:115611600-115626800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr9:115611600-115630200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr9:115611600-115634200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr9:115611800-115616000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr9:115611800-115617000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:115611800-115617000	Strong transcription	Stomach Smooth Muscle	stomach
34	chr9:115611800-115630200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr9:115612000-115617000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr9:115612000-115620600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:115612000-115634600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr9:115612200-115617000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr9:115612200-115617400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr9:115612200-115620400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr9:115612400-115617200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:115612400-115617200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr9:115612600-115616200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr9:115612600-115617600	Strong transcription	Primary T cells from cord blood	blood
45	chr9:115613000-115615600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr9:115613000-115617200	Strong transcription	Liver	Liver
47	chr9:115613000-115617200	Strong transcription	Duodenum Mucosa	Duodenum
48	chr9:115613000-115617200	Strong transcription	Gastric	stomach
49	chr9:115613000-115617400	Strong transcription	Spleen	Spleen
50	chr9:115613200-115615600	Strong transcription	Rectal Mucosa Donor 31	rectum

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