Variant report

Variant	rs6446273
Chromosome Location	chr3:49465145-49465146
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr3:49465051-49465339	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr3:49465106-49465249	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr3:49465051-49465340	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr3:49465051-49465334	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49376764..49379634-chr3:49465144..49467494,3	MCF-7	breast:
2	chr3:49463180..49464811-chr3:49464830..49467753,3	K562	blood:
3	chr3:49457686..49462880-chr3:49464384..49468098,7	MCF-7	breast:
4	chr3:49460720..49464051-chr3:49464777..49467713,3	MCF-7	breast:
5	chr3:49447469..49451415-chr3:49463621..49468909,12	K562	blood:

Variant related genes	Relation type
NICN1	TF binding region
AMT	TF binding region
ENSG00000114316	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000235261	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000145029	Chromatin interaction
ENSG00000145020	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs11130197	1.00[YRI][hapmap]
rs11130201	0.89[AFR][1000 genomes]
rs11708174	1.00[YRI][hapmap]
rs11717485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1522929	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1568663	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080495	0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080510	0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080567	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080664	0.92[YRI][hapmap];0.92[AFR][1000 genomes]
rs1996874	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2131107	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2311794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2311801	0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2329024	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28615670	1.00[EUR][1000 genomes]
rs3870334	0.82[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3870340	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3912831	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4241409	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4452334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4527417	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855856	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855857	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4855872	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855876	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855879	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55677747	0.81[AFR][1000 genomes]
rs55808753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55990645	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56101322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56760510	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56897974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59579780	0.86[AFR][1000 genomes]
rs60011446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61749312	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446269	0.97[AFR][1000 genomes]
rs6446270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446278	0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446279	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446280	0.92[AFR][1000 genomes]
rs6446281	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446282	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446283	1.00[EUR][1000 genomes]
rs6762593	1.00[YRI][hapmap]
rs6766297	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787665	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6793124	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6797164	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936890	1.00[EUR][1000 genomes]
rs73830703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831434	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831435	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831436	1.00[EUR][1000 genomes]
rs73831437	1.00[EUR][1000 genomes]
rs73831438	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831439	0.86[AFR][1000 genomes]
rs73831440	0.86[AFR][1000 genomes]
rs73831441	0.86[AFR][1000 genomes]
rs73831442	0.92[AFR][1000 genomes]
rs7646393	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8179172	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9311441	1.00[AFR][1000 genomes]
rs9811460	1.00[EUR][1000 genomes]
rs9814413	1.00[EUR][1000 genomes]
rs9830627	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9837396	1.00[EUR][1000 genomes]
rs9849446	1.00[EUR][1000 genomes]
rs9861805	0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869504	1.00[EUR][1000 genomes]
rs9875203	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv963482	chr3:49459177-49486938	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 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	chr3:49451200-49466200	Weak transcription	Psoas Muscle	Psoas
2	chr3:49455600-49466200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:49457400-49466000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:49457600-49465400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr3:49459200-49466200	Weak transcription	HUVEC	blood vessel
6	chr3:49459400-49465800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr3:49459600-49465200	Weak transcription	Hela-S3	cervix
8	chr3:49459600-49465600	Weak transcription	NHDF-Ad	bronchial
9	chr3:49459600-49466200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:49459600-49466200	Weak transcription	HMEC	breast
11	chr3:49459800-49465600	Weak transcription	NHEK	skin
12	chr3:49460200-49466000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:49460400-49465800	Weak transcription	Brain Angular Gyrus	brain
14	chr3:49460400-49465800	Weak transcription	Right Atrium	heart
15	chr3:49460400-49466200	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:49460600-49465600	Weak transcription	Esophagus	oesophagus
17	chr3:49460600-49465600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:49460600-49465600	Weak transcription	A549	lung
19	chr3:49460600-49465800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:49460600-49465800	Weak transcription	Brain Substantia Nigra	brain
21	chr3:49460600-49465800	Weak transcription	Fetal Brain Male	brain
22	chr3:49460600-49466000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:49460600-49466000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:49460600-49466000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:49460600-49466000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:49460600-49466200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:49460600-49466200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:49460600-49466200	Weak transcription	Small Intestine	intestine
29	chr3:49460600-49466200	Weak transcription	Stomach Mucosa	stomach
30	chr3:49460600-49466200	Weak transcription	HSMM	muscle
31	chr3:49460600-49466200	Weak transcription	Osteobl	bone
32	chr3:49460800-49465600	Weak transcription	NH-A	brain
33	chr3:49460800-49465800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr3:49460800-49466000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:49460800-49466000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:49460800-49466000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:49460800-49466200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:49460800-49466200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:49460800-49466200	Weak transcription	Fetal Heart	heart
40	chr3:49460800-49466200	Weak transcription	Fetal Kidney	kidney
41	chr3:49460800-49466200	Weak transcription	HSMMtube	muscle
42	chr3:49461200-49465200	Weak transcription	HepG2	liver
43	chr3:49462000-49465800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr3:49462200-49465600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr3:49462200-49465800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:49462400-49465800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:49462600-49466200	Weak transcription	NHLF	lung
48	chr3:49462800-49466000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:49463200-49465200	Weak transcription	GM12878-XiMat	blood
50	chr3:49463200-49466200	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links