Variant report

Variant	rs35647517
Chromosome Location	chr5:49726573-49726574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:49721397..49723979-chr5:49726310..49728493,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs13154421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13158256	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13160401	1.00[AFR][1000 genomes]
rs13165145	1.00[AFR][1000 genomes]
rs13169411	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13174803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13185634	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13189140	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17192300	0.92[EUR][1000 genomes]
rs17192503	0.92[EUR][1000 genomes]
rs17800685	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1962207	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34434894	1.00[AFR][1000 genomes]
rs34836131	1.00[AFR][1000 genomes]
rs35005767	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35290633	1.00[AFR][1000 genomes]
rs35703604	0.82[EUR][1000 genomes]
rs35831659	0.84[EUR][1000 genomes]
rs36108557	0.85[EUR][1000 genomes]
rs363983	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3860733	0.80[AMR][1000 genomes]
rs58931923	0.83[EUR][1000 genomes]
rs61133464	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6893317	0.97[EUR][1000 genomes]
rs71631457	1.00[AFR][1000 genomes]
rs71631459	1.00[AFR][1000 genomes]
rs71631461	0.80[AMR][1000 genomes]
rs71631464	0.83[EUR][1000 genomes]
rs71631467	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71631474	0.83[EUR][1000 genomes]
rs71631475	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7709512	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032003	chr5:49455624-49881491	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1023981	chr5:49584188-49871537	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv537757	chr5:49584188-49871537	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv916441	chr5:49584313-49831223	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35647517	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49703200-49727000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:49718400-49727400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr5:49719200-49726800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:49720400-49736400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:49720400-49736400	Weak transcription	Spleen	Spleen
6	chr5:49720600-49726800	Weak transcription	HSMMtube	muscle
7	chr5:49723600-49735200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr5:49723800-49727400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr5:49724000-49733400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr5:49724200-49727400	Enhancers	Primary B cells from peripheral blood	blood
11	chr5:49724200-49727400	Enhancers	Primary T cells fromperipheralblood	blood
12	chr5:49724200-49731000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:49724200-49735800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:49724400-49727800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr5:49724400-49730400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr5:49724600-49727200	Enhancers	Primary hematopoietic stem cells	blood
17	chr5:49724600-49728000	Enhancers	Primary B cells from cord blood	blood
18	chr5:49724600-49729200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr5:49724600-49730400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr5:49724600-49732400	Enhancers	Primary T cells from cord blood	blood
21	chr5:49724800-49727400	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr5:49724800-49732800	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr5:49725000-49729000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr5:49725600-49727200	Flanking Active TSS	Dnd41	blood
25	chr5:49725600-49727200	Enhancers	HSMM	muscle
26	chr5:49725600-49727400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:49725800-49726800	Enhancers	Muscle Satellite Cultured Cells	--
28	chr5:49725800-49727400	Enhancers	Duodenum Mucosa	Duodenum
29	chr5:49726000-49726600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:49726000-49726600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:49726000-49726600	Enhancers	NHEK	skin
32	chr5:49726000-49727400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr5:49726000-49731400	Weak transcription	Small Intestine	intestine
34	chr5:49726200-49726600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:49726200-49726600	Enhancers	HMEC	breast
36	chr5:49726200-49726800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr5:49726200-49727400	Enhancers	Fetal Thymus	thymus
38	chr5:49726400-49726800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr5:49726400-49727200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:49726400-49727200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr5:49726400-49727200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr5:49726400-49727200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr5:49726400-49727200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:49726400-49727200	Enhancers	Adipose Nuclei	Adipose
45	chr5:49726400-49727800	Enhancers	Osteobl	bone
46	chr5:49726400-49728600	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr5:49726400-49735000	Enhancers	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links