Variant report

Variant	rs57096664
Chromosome Location	chr9:98618269-98618270
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	GATA3	chr9:98618186-98619984	SK-N-SH	brain:	n/a	chr9:98618252-98618262 chr9:98618253-98618262 chr9:98618499-98618509

No.	Distal block	Cell Line	Cell type
1	chr9:98617573..98619992-chr9:98637959..98639556,2	MCF-7	breast:
2	chr9:98614433..98624477-chr9:98629889..98639636,23	MCF-7	breast:
3	chr9:98611430..98613498-chr9:98617563..98619978,2	MCF-7	breast:
4	chr9:98268488..98270508-chr9:98617458..98619875,2	K562	blood:
5	chr9:98611900..98615420-chr9:98615884..98619826,3	MCF-7	breast:
6	chr9:98583856..98586047-chr9:98617880..98619976,2	MCF-7	breast:

Variant related genes	Relation type
RNU2-46P	TF binding region
ENSG00000182150	Chromatin interaction
ENSG00000185920	Chromatin interaction
ENSG00000271155	Chromatin interaction
ENSG00000175611	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12003772	0.92[ASN][1000 genomes]
rs12551596	0.97[ASN][1000 genomes]
rs12551880	0.93[ASN][1000 genomes]
rs12554182	0.90[ASN][1000 genomes]
rs12555687	0.97[ASN][1000 genomes]
rs1413178	0.97[ASN][1000 genomes]
rs16910333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16910342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16910409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16910427	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17303324	0.93[ASN][1000 genomes]
rs2297009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3739755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3739756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4742763	0.93[ASN][1000 genomes]
rs4742769	0.97[ASN][1000 genomes]
rs4742801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743327	0.86[ASN][1000 genomes]
rs4743351	0.91[ASN][1000 genomes]
rs4743383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4743469	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4743507	1.00[AFR][1000 genomes]
rs4743508	1.00[AFR][1000 genomes]
rs55651016	1.00[ASN][1000 genomes]
rs55770584	0.93[ASN][1000 genomes]
rs55781050	0.97[ASN][1000 genomes]
rs55797980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55849673	1.00[AFR][1000 genomes]
rs55865494	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55881510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56063686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56070531	0.93[ASN][1000 genomes]
rs56110216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56125887	0.97[ASN][1000 genomes]
rs56319412	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs56372801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56403401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57287260	1.00[AFR][1000 genomes]
rs58654424	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs59046245	0.97[ASN][1000 genomes]
rs59189545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60351339	1.00[AFR][1000 genomes]
rs61036807	0.97[ASN][1000 genomes]
rs61093440	0.97[ASN][1000 genomes]
rs9721742	0.82[ASN][1000 genomes]
rs9792431	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9792684	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98596200-98619200	Weak transcription	Fetal Heart	heart
2	chr9:98596400-98619400	Weak transcription	Right Ventricle	heart
3	chr9:98602000-98632800	Weak transcription	Left Ventricle	heart
4	chr9:98602000-98636000	Weak transcription	Lung	lung
5	chr9:98602400-98619400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr9:98602600-98618800	Weak transcription	Fetal Muscle Leg	muscle
7	chr9:98602600-98619400	Weak transcription	Psoas Muscle	Psoas
8	chr9:98602600-98620200	Weak transcription	Small Intestine	intestine
9	chr9:98602800-98619000	Weak transcription	Ovary	ovary
10	chr9:98604400-98621200	Weak transcription	Primary T cells from cord blood	blood
11	chr9:98607400-98621600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr9:98609000-98619400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr9:98610200-98636200	Weak transcription	Brain Germinal Matrix	brain
14	chr9:98610200-98636800	Weak transcription	Gastric	stomach
15	chr9:98610400-98618800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:98610600-98618800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:98610600-98619400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:98611200-98620200	Weak transcription	Primary B cells from cord blood	blood
19	chr9:98611200-98620400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:98611400-98619200	Weak transcription	Fetal Intestine Small	intestine
21	chr9:98613400-98632800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr9:98614200-98620400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:98614400-98620200	Enhancers	NHEK	skin
24	chr9:98614600-98620000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr9:98615000-98619400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr9:98615200-98620400	Enhancers	Muscle Satellite Cultured Cells	--
27	chr9:98615200-98624400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:98615400-98619200	Weak transcription	HSMMtube	muscle
29	chr9:98615400-98619400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr9:98615400-98624000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:98615600-98619400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr9:98615800-98618400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr9:98615800-98618800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr9:98615800-98619400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr9:98615800-98619400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:98615800-98620200	Weak transcription	K562	blood
37	chr9:98616000-98620600	Enhancers	Fetal Lung	lung
38	chr9:98616400-98620400	Enhancers	Fetal Stomach	stomach
39	chr9:98616600-98620200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr9:98616600-98620200	Enhancers	HSMM	muscle
41	chr9:98617000-98619800	Enhancers	GM12878-XiMat	blood
42	chr9:98617000-98634200	Weak transcription	Fetal Kidney	kidney
43	chr9:98617200-98618600	Weak transcription	Hela-S3	cervix
44	chr9:98617200-98618800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:98617200-98620200	Enhancers	HUVEC	blood vessel
46	chr9:98617600-98618400	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr9:98617600-98618600	Weak transcription	HMEC	breast
48	chr9:98617800-98618800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr9:98617800-98619000	Weak transcription	A549	lung
50	chr9:98617800-98619200	Weak transcription	NH-A	brain

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