Variant report

Variant	rs10981517
Chromosome Location	chr9:115599416-115599417
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	CEBPB	chr9:115599414-115599451	HepG2	liver:	n/a	n/a

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
ENSG00000148158	Chromatin interaction
ENSG00000226609	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10759584	0.87[ASN][1000 genomes]
rs10759587	0.82[AFR][1000 genomes]
rs10817380	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10817381	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10817383	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10817385	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10817387	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10817388	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10817390	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10817393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981497	1.00[EUR][1000 genomes]
rs10981500	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10981501	1.00[EUR][1000 genomes]
rs10981506	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10981510	0.93[ASN][1000 genomes]
rs10981512	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10981513	0.90[AFR][1000 genomes]
rs10981520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981525	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981527	0.97[ASN][1000 genomes]
rs11790110	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11792606	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11794186	1.00[EUR][1000 genomes]
rs12235123	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12685108	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1361719	0.84[ASN][1000 genomes]
rs1361720	0.82[ASN][1000 genomes]
rs1418408	0.82[AFR][1000 genomes]
rs1539345	0.82[AFR][1000 genomes]
rs2645993	0.84[ASN][1000 genomes]
rs28494060	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4979148	0.87[ASN][1000 genomes]
rs4979150	0.87[ASN][1000 genomes]
rs4979153	0.87[ASN][1000 genomes]
rs4979156	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs59721032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859381	0.87[ASN][1000 genomes]
rs7863952	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7868830	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7872308	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs787269	0.87[ASN][1000 genomes]
rs787270	0.87[ASN][1000 genomes]
rs787271	0.87[ASN][1000 genomes]
rs787272	0.87[ASN][1000 genomes]
rs787274	0.87[ASN][1000 genomes]
rs787275	0.87[ASN][1000 genomes]
rs787276	0.87[ASN][1000 genomes]
rs787279	0.84[ASN][1000 genomes]
rs787280	0.84[ASN][1000 genomes]
rs787284	0.82[ASN][1000 genomes]
rs787295	0.84[ASN][1000 genomes]
rs787297	0.84[ASN][1000 genomes]
rs787298	0.84[ASN][1000 genomes]
rs787301	0.84[ASN][1000 genomes]
rs7873644	0.82[AFR][1000 genomes]
rs813101	0.84[ASN][1000 genomes]
rs9299210	0.82[AFR][1000 genomes]
rs999018	0.82[AFR][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: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	chr9:115592400-115600000	Weak transcription	Dnd41	blood
19	chr9:115592600-115607200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr9:115593200-115611000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr9:115593400-115602600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:115593600-115599600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:115593600-115607200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr9:115594000-115602800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr9:115594200-115600600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr9:115594200-115600800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:115594200-115603000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr9:115594200-115607200	Weak transcription	Fetal Thymus	thymus
29	chr9:115594200-115610800	Weak transcription	Esophagus	oesophagus
30	chr9:115594200-115616000	Weak transcription	Small Intestine	intestine
31	chr9:115594200-115620400	Weak transcription	Thymus	Thymus
32	chr9:115594200-115634400	Weak transcription	NH-A	brain
33	chr9:115594400-115601400	Weak transcription	Fetal Brain Female	brain
34	chr9:115594400-115608600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr9:115594400-115626800	Weak transcription	Colon Smooth Muscle	Colon
36	chr9:115594600-115599600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr9:115594600-115600400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr9:115594600-115607200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr9:115594600-115607200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr9:115595600-115602400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr9:115596200-115604000	Strong transcription	Fetal Stomach	stomach
42	chr9:115596400-115599600	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr9:115596400-115613600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr9:115596600-115601200	Enhancers	Stomach Mucosa	stomach
45	chr9:115597000-115599600	Strong transcription	Brain Anterior Caudate	brain
46	chr9:115597400-115599600	Genic enhancers	Fetal Intestine Small	intestine
47	chr9:115597400-115605600	Strong transcription	Primary T cells from cord blood	blood
48	chr9:115597600-115600600	Weak transcription	HSMMtube	muscle
49	chr9:115597800-115599800	Enhancers	Fetal Intestine Large	intestine
50	chr9:115598000-115599600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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