Variant report

Variant	rs3733103
Chromosome Location	chr3:45962595-45962596
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:45961740..45963512-chr3:45972118..45973716,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1072755	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130080	0.88[CEU][hapmap]
rs12495073	0.84[CEU][hapmap]
rs12630101	0.92[CEU][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12635494	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12635657	0.90[CEU][hapmap]
rs12639598	0.88[CEU][hapmap];0.85[MEX][hapmap]
rs13066048	0.92[CEU][hapmap];0.82[CHB][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13091821	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13091979	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1532071	0.84[ASN][1000 genomes]
rs1552489	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1552490	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1601867	0.82[ASN][1000 genomes]
rs1994488	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1994489	0.84[ASN][1000 genomes]
rs1994490	0.84[MEX][hapmap]
rs2054866	0.92[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2171530	0.97[ASN][1000 genomes]
rs2234358	0.82[CHB][hapmap];0.90[CHD][hapmap];0.90[MEX][hapmap];0.81[ASN][1000 genomes]
rs2248228	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291470	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35465473	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3774634	0.92[CEU][hapmap];0.85[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3774635	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3774639	0.92[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.90[MEX][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3796373	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3796375	0.88[CEU][hapmap];0.85[MEX][hapmap]
rs4535265	0.88[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4682799	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[MEX][hapmap];0.84[ASN][1000 genomes]
rs4682800	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs4683147	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs4683148	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683149	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4683152	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4683154	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4683156	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4683157	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6800954	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs7129	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs730983	0.88[CEU][hapmap]
rs737452	0.88[CEU][hapmap]
rs751552	0.88[CEU][hapmap];0.85[MEX][hapmap]
rs751553	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs9311380	0.84[ASN][1000 genomes]
rs936938	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9824253	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9831315	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45949800-45962600	Weak transcription	HepG2	liver
2	chr3:45952800-45963600	Weak transcription	Psoas Muscle	Psoas
3	chr3:45952800-45964600	Weak transcription	Fetal Heart	heart
4	chr3:45957400-45963000	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:45957600-45965000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:45957800-45962600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:45957800-45962600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:45957800-45962600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:45957800-45963000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:45957800-45963000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:45957800-45963600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:45957800-45963600	Weak transcription	Colonic Mucosa	Colon
13	chr3:45957800-45969000	Weak transcription	K562	blood
14	chr3:45957800-45971200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:45958000-45962800	Weak transcription	Brain Germinal Matrix	brain
16	chr3:45958000-45964400	Weak transcription	Stomach Mucosa	stomach
17	chr3:45958000-45964600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:45958000-45964800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:45958000-45965000	Weak transcription	Osteobl	bone
20	chr3:45958000-45965200	Weak transcription	HSMM	muscle
21	chr3:45958000-45969000	Weak transcription	NH-A	brain
22	chr3:45958000-45980800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:45958200-45963200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:45958200-45963400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:45958400-45963000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:45958400-45966200	Strong transcription	Stomach Smooth Muscle	stomach
27	chr3:45958400-45974200	Strong transcription	Fetal Stomach	stomach
28	chr3:45958600-45963000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:45958600-45968800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr3:45958600-45970000	Weak transcription	Small Intestine	intestine
31	chr3:45958800-45962600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr3:45958800-45964600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:45958800-45980000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:45958800-45980200	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:45958800-45988000	Weak transcription	HUVEC	blood vessel
36	chr3:45959000-45962800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr3:45959000-45966000	Genic enhancers	Fetal Thymus	thymus
38	chr3:45959000-45973600	Weak transcription	Fetal Kidney	kidney
39	chr3:45959200-45962600	Weak transcription	NHEK	skin
40	chr3:45959200-45979800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr3:45959200-45980400	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:45959400-45962800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr3:45959400-45962800	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr3:45959400-45965000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:45959400-45965200	Weak transcription	HMEC	breast
46	chr3:45959400-45965800	Genic enhancers	Thymus	Thymus
47	chr3:45959400-45965800	Genic enhancers	Dnd41	blood
48	chr3:45959400-45966000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr3:45959400-45971800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:45959400-45973400	Strong transcription	Primary monocytes fromperipheralblood	blood

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