Variant report

Variant	rs9860797
Chromosome Location	chr3:89164099-89164100
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:88268096..88268898-chr3:89163502..89164670,4	MCF-7	breast:
2	chr3:88252276..88253622-chr3:89163430..89164364,7	MCF-7	breast:
3	chr3:88690003..88690853-chr3:89163399..89164385,5	MCF-7	breast:
4	chr3:89163095..89164119-chr3:89900902..89901799,5	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11128071	0.86[YRI][hapmap]
rs12629427	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12637863	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13315867	0.92[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13326166	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4425279	0.82[CHB][hapmap];0.89[YRI][hapmap]
rs59012690	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6551393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551394	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6551396	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6551400	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6551401	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6768846	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6802483	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72919895	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72921746	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7374085	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7433757	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7611735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7612982	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7630371	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7631328	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7639401	0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7641811	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7647240	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9310117	0.80[YRI][hapmap]
rs9809011	0.81[YRI][hapmap]
rs9810366	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs9815025	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9821502	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9832319	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9834174	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9834433	0.81[CEU][hapmap];0.84[CHB][hapmap];0.80[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9838527	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9842523	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9843199	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9848187	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9854754	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9868838	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9878894	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9883005	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9883387	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9883681	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.89[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	nsv877159	chr3:89018866-89207222	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv998460	chr3:89064073-89188335	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv536638	chr3:89064073-89188335	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv834760	chr3:89085529-89299398	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89163000-89164200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr3:89163000-89164200	Active TSS	Right Atrium	heart
3	chr3:89163000-89164400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr3:89163000-89164400	Active TSS	Brain Anterior Caudate	brain
5	chr3:89163000-89164400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:89163200-89164200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:89163200-89164200	Bivalent/Poised TSS	Fetal Kidney	kidney
8	chr3:89163200-89164200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
9	chr3:89163200-89164200	Flanking Active TSS	HMEC	breast
10	chr3:89163200-89164400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:89163200-89164400	Active TSS	Brain Angular Gyrus	brain
12	chr3:89163400-89164200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr3:89163400-89164200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:89163400-89164200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:89163400-89164200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:89163400-89164200	Enhancers	Liver	Liver
17	chr3:89163400-89164200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
18	chr3:89163400-89164200	Active TSS	Rectal Smooth Muscle	rectum
19	chr3:89163400-89164200	Active TSS	Right Ventricle	heart
20	chr3:89163400-89164200	Active TSS	NHDF-Ad	bronchial
21	chr3:89163400-89164400	Active TSS	Fetal Brain Male	brain
22	chr3:89163600-89164200	Active TSS	H9 Cell Line	embryonic stem cell
23	chr3:89163600-89164200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
24	chr3:89163600-89164200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
25	chr3:89163600-89164200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr3:89163600-89164200	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
27	chr3:89163600-89164200	Active TSS	Duodenum Mucosa	Duodenum
28	chr3:89163600-89164200	Active TSS	Esophagus	oesophagus
29	chr3:89163600-89164200	Bivalent/Poised TSS	Fetal Thymus	thymus
30	chr3:89163600-89164200	Active TSS	NHLF	lung
31	chr3:89163600-89164400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
32	chr3:89163600-89164400	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr3:89163800-89164200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:89163800-89164200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:89163800-89164200	Enhancers	Primary B cells from peripheral blood	blood
36	chr3:89163800-89164200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:89163800-89164200	Active TSS	Colonic Mucosa	Colon
38	chr3:89163800-89164200	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr3:89163800-89164200	Active TSS	Fetal Brain Female	brain
40	chr3:89163800-89164200	Bivalent/Poised TSS	Fetal Lung	lung
41	chr3:89163800-89164200	Enhancers	Placenta Amnion	Placenta Amnion
42	chr3:89163800-89164200	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr3:89163800-89164400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
44	chr3:89163800-89164400	Enhancers	Fetal Heart	heart
45	chr3:89163800-89164600	Flanking Active TSS	Brain Germinal Matrix	brain
46	chr3:89164000-89164200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
47	chr3:89164000-89164200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:89164000-89164200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:89164000-89164200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:89164000-89164200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung

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