Variant report

Variant	rs10981516
Chromosome Location	chr9:115598844-115598845
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	ARID3A	chr9:115598674-115599001	HepG2	liver:	n/a	n/a
2	RFX5	chr9:115598744-115599030	HepG2	liver:	n/a	n/a
3	MAFF	chr9:115598666-115599080	HepG2	liver:	n/a	chr9:115598883-115598897
4	MAFK	chr9:115598697-115599031	HepG2	liver:	n/a	chr9:115598884-115598894
5	FOXA1	chr9:115598689-115599186	HepG2	liver:	n/a	chr9:115599025-115599037
6	FOXA1	chr9:115598646-115599123	HepG2	liver:	n/a	chr9:115599025-115599037
7	HNF4A	chr9:115598710-115599031	HepG2	liver:	n/a	chr9:115598871-115598885 chr9:115598873-115598881
8	RCOR1	chr9:115598724-115599059	HepG2	liver:	n/a	n/a
9	TEAD4	chr9:115598643-115599053	HepG2	liver:	n/a	n/a
10	MAFK	chr9:115598661-115599042	HepG2	liver:	n/a	chr9:115598884-115598894
11	HNF4A	chr9:115598695-115598974	HepG2	liver:	n/a	chr9:115598871-115598885 chr9:115598873-115598881
12	FOXA1	chr9:115598639-115599094	HepG2	liver:	n/a	chr9:115599025-115599037
13	FOXA2	chr9:115598690-115599041	HepG2	liver:	n/a	chr9:115599025-115599037
14	FOXA1	chr9:115598661-115599170	HepG2	liver:	n/a	chr9:115599025-115599037

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:115511814..115513808-chr9:115597471..115599757,2	MCF-7	breast:
2	chr9:115581292..115584107-chr9:115597875..115599534,2	MCF-7	breast:

Variant related genes	Relation type
SNX30	TF binding region
ENSG00000226609	Chromatin interaction
ENSG00000148158	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10117017	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10117709	0.96[ASN][1000 genomes]
rs10122712	0.99[ASN][1000 genomes]
rs10513169	0.93[EUR][1000 genomes]
rs10732374	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10733595	0.94[ASN][1000 genomes]
rs10739371	0.91[ASN][1000 genomes]
rs10759587	0.94[ASN][1000 genomes]
rs10759588	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]
rs10817395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817396	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10981513	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981515	0.91[ASN][1000 genomes]
rs10981519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981523	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	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	0.94[ASN][1000 genomes]
rs1539345	0.99[ASN][1000 genomes]
rs1573055	0.92[EUR][1000 genomes]
rs1573056	0.93[EUR][1000 genomes]
rs17742501	0.86[EUR][1000 genomes]
rs17742994	0.86[EUR][1000 genomes]
rs17743418	0.93[EUR][1000 genomes]
rs17743824	0.96[EUR][1000 genomes]
rs17821593	0.86[EUR][1000 genomes]
rs2000204	0.89[ASN][1000 genomes]
rs2096186	0.84[ASN][1000 genomes]
rs2096187	0.80[ASN][1000 genomes]
rs2153839	0.91[ASN][1000 genomes]
rs2185767	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796024	0.89[ASN][1000 genomes]
rs41280189	0.96[EUR][1000 genomes]
rs4276760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4978504	0.90[ASN][1000 genomes]
rs4979158	0.94[ASN][1000 genomes]
rs4979162	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4979163	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4979164	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4979166	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	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7871799	0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs787282	0.87[ASN][1000 genomes]
rs787283	0.87[ASN][1000 genomes]
rs787288	0.87[ASN][1000 genomes]
rs7873644	0.94[ASN][1000 genomes]
rs870078	0.87[ASN][1000 genomes]
rs883462	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	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

No data

Chromatin state (count:120 , 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	chr9:115581200-115599200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:115582200-115608600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr9:115582400-115600600	Weak transcription	HSMM	muscle
13	chr9:115582400-115608600	Weak transcription	NHLF	lung
14	chr9:115582400-115609000	Weak transcription	NHDF-Ad	bronchial
15	chr9:115582400-115630000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr9:115584400-115608800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:115591200-115606800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr9:115591400-115623200	Weak transcription	Fetal Heart	heart
19	chr9:115592400-115600000	Weak transcription	Dnd41	blood
20	chr9:115592600-115607200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr9:115593200-115611000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr9:115593400-115602600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr9:115593600-115599600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:115593600-115607200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr9:115593800-115599000	Weak transcription	Primary B cells from cord blood	blood
26	chr9:115594000-115602800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:115594200-115600600	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr9:115594200-115600800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:115594200-115603000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr9:115594200-115607200	Weak transcription	Fetal Thymus	thymus
31	chr9:115594200-115610800	Weak transcription	Esophagus	oesophagus
32	chr9:115594200-115616000	Weak transcription	Small Intestine	intestine
33	chr9:115594200-115620400	Weak transcription	Thymus	Thymus
34	chr9:115594200-115634400	Weak transcription	NH-A	brain
35	chr9:115594400-115601400	Weak transcription	Fetal Brain Female	brain
36	chr9:115594400-115608600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr9:115594400-115626800	Weak transcription	Colon Smooth Muscle	Colon
38	chr9:115594600-115599600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr9:115594600-115600400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr9:115594600-115607200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr9:115594600-115607200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr9:115595600-115602400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr9:115596200-115604000	Strong transcription	Fetal Stomach	stomach
44	chr9:115596400-115599400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr9:115596400-115599600	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr9:115596400-115613600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr9:115596600-115601200	Enhancers	Stomach Mucosa	stomach
48	chr9:115597000-115599600	Strong transcription	Brain Anterior Caudate	brain
49	chr9:115597200-115599200	Strong transcription	Brain Substantia Nigra	brain
50	chr9:115597400-115599000	Enhancers	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links