Variant report

Variant	rs9879593
Chromosome Location	chr3:118927015-118927016
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:118925125..118927073-chr3:118927779..118929469,2	MCF-7	breast:
2	chr3:118924439..118927161-chr3:118936255..118939127,2	MCF-7	breast:
3	chr3:118925359..118927166-chr3:118958232..118960425,2	MCF-7	breast:
4	chr3:118926942..118931120-chr3:118957602..118962247,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121578	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10511384	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12690556	0.89[ASN][1000 genomes]
rs12695382	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12695383	0.95[ASN][1000 genomes]
rs13070981	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13091429	0.95[ASN][1000 genomes]
rs13094747	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13098659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2001286	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28587867	0.87[ASN][1000 genomes]
rs28668839	0.90[ASN][1000 genomes]
rs28885082	0.89[ASN][1000 genomes]
rs35816234	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3752376	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3752377	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796358	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57446248	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59140322	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59448071	0.95[ASN][1000 genomes]
rs6438503	0.94[CEU][hapmap]
rs68103027	0.85[ASN][1000 genomes]
rs71325367	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7650288	0.96[ASN][1000 genomes]
rs9289125	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9812715	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9818595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9824387	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9832248	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9834466	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835060	0.94[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs9836230	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9837110	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9844382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9849672	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9850349	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9857127	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9858124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9862321	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9867379	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9869645	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs9874573	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9878996	1.00[CEU][hapmap]
rs9881379	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9881947	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv591362	chr3:118906442-118948155	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118904600-118936400	Weak transcription	Gastric	stomach
2	chr3:118908400-118928200	Weak transcription	Fetal Stomach	stomach
3	chr3:118911800-118932600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:118915200-118928400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:118915200-118934800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:118920400-118930400	Weak transcription	Fetal Kidney	kidney
7	chr3:118921000-118928000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:118921400-118931200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:118922200-118927400	Weak transcription	HSMM	muscle
10	chr3:118922600-118929000	Weak transcription	Spleen	Spleen
11	chr3:118923000-118927600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr3:118923000-118929000	Weak transcription	Brain Germinal Matrix	brain
13	chr3:118923200-118927400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:118923400-118927400	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr3:118923600-118930800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:118923800-118931600	Enhancers	Stomach Mucosa	stomach
17	chr3:118924200-118927200	Enhancers	Fetal Thymus	thymus
18	chr3:118924200-118927800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr3:118924200-118931600	Weak transcription	NHDF-Ad	bronchial
20	chr3:118924400-118927600	Weak transcription	Aorta	Aorta
21	chr3:118924400-118928200	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr3:118924400-118929200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:118924400-118929800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:118924400-118933200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:118924400-118959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr3:118924600-118927200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:118924600-118927800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:118924600-118928000	Weak transcription	Ovary	ovary
29	chr3:118924600-118929000	Weak transcription	Colonic Mucosa	Colon
30	chr3:118924600-118930000	Weak transcription	Osteobl	bone
31	chr3:118924600-118930200	Weak transcription	Fetal Lung	lung
32	chr3:118924600-118945600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr3:118924800-118927200	Enhancers	NHEK	skin
34	chr3:118924800-118927400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:118924800-118928000	Weak transcription	Fetal Muscle Leg	muscle
36	chr3:118924800-118928400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:118924800-118929400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:118924800-118931200	Weak transcription	Right Ventricle	heart
39	chr3:118925200-118927200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:118925400-118927400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr3:118925600-118927200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:118925600-118927200	Weak transcription	Liver	Liver
43	chr3:118925600-118927200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr3:118925600-118928400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:118925600-118929000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:118925600-118929000	Weak transcription	HepG2	liver
47	chr3:118925600-118929200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:118925600-118930000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr3:118925800-118927400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:118925800-118928000	Weak transcription	Fetal Brain Female	brain

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