Variant report

Variant	rs17393059
Chromosome Location	chr3:99761908-99761909
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99756496..99759063-chr3:99760481..99762156,3	MCF-7	breast:
2	chr3:99760023..99762628-chr3:99763026..99765995,4	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10049383	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1017968	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10212525	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1021341	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10511177	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13064704	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13069311	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13093776	0.81[EUR][1000 genomes]
rs13093838	0.83[AMR][1000 genomes]
rs13323143	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1489816	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17379739	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17392948	0.83[AMR][1000 genomes]
rs2291494	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291495	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28503408	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28714363	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34922392	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34996634	0.83[AMR][1000 genomes]
rs35154249	0.83[AMR][1000 genomes]
rs35521705	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35669453	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35844878	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35885423	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4279135	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4571265	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4928234	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62285461	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62285462	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62285471	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62285473	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62285478	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6790535	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6790877	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802422	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806178	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6807176	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71313585	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610486	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7616988	0.81[EUR][1000 genomes]
rs7620228	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7627991	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs923470	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923471	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810235	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9814359	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9815439	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9823908	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9828079	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9832186	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9833888	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9833980	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834484	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9837602	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9841186	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9851645	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852435	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9853823	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9864437	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873709	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9873878	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9875640	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9875664	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9878931	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv999332	chr3:99690207-99774720	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99713600-99787800	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99741200-99766800	Weak transcription	Right Ventricle	heart
3	chr3:99742400-99766400	Weak transcription	Aorta	Aorta
4	chr3:99746600-99762200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:99752200-99774600	Weak transcription	Gastric	stomach
6	chr3:99757600-99762400	Enhancers	Fetal Intestine Large	intestine
7	chr3:99757800-99766800	Weak transcription	Pancreas	Pancrea
8	chr3:99758400-99762600	Enhancers	NHLF	lung
9	chr3:99758800-99762000	Enhancers	Fetal Stomach	stomach
10	chr3:99758800-99762000	Enhancers	Stomach Smooth Muscle	stomach
11	chr3:99758800-99763800	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr3:99759000-99762200	Enhancers	Colon Smooth Muscle	Colon
13	chr3:99759000-99762400	Enhancers	Rectal Smooth Muscle	rectum
14	chr3:99759000-99762800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:99759000-99762800	Enhancers	HMEC	breast
16	chr3:99759000-99763400	Enhancers	NHEK	skin
17	chr3:99759000-99766600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:99759200-99762000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:99759200-99762400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:99759200-99762400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:99759200-99762600	Enhancers	NH-A	brain
22	chr3:99759200-99763200	Enhancers	Adipose Nuclei	Adipose
23	chr3:99759200-99766200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:99759200-99766400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr3:99759200-99768200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:99759400-99762000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:99759400-99762400	Enhancers	A549	lung
28	chr3:99759400-99762600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:99759600-99762000	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr3:99759600-99762400	Enhancers	Fetal Intestine Small	intestine
31	chr3:99759600-99764000	Weak transcription	Fetal Brain Male	brain
32	chr3:99759800-99762200	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr3:99760000-99762000	Enhancers	HepG2	liver
34	chr3:99760000-99762200	Weak transcription	GM12878-XiMat	blood
35	chr3:99760200-99763800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:99760200-99764000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:99760200-99764400	Weak transcription	Left Ventricle	heart
38	chr3:99760800-99764400	Weak transcription	Fetal Muscle Leg	muscle
39	chr3:99760800-99764600	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:99760800-99764600	Weak transcription	Right Atrium	heart
41	chr3:99760800-99765000	Weak transcription	Stomach Mucosa	stomach
42	chr3:99761000-99762200	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr3:99761200-99762000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:99761200-99762200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:99761200-99762400	Enhancers	Hela-S3	cervix
46	chr3:99761200-99763800	Enhancers	HUVEC	blood vessel
47	chr3:99761200-99765600	Enhancers	Primary B cells from cord blood	blood
48	chr3:99761200-99766200	Enhancers	Primary B cells from peripheral blood	blood
49	chr3:99761400-99762000	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr3:99761400-99762000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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