Variant report

Variant	rs1749945
Chromosome Location	chr14:37227275-37227276
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	chr14:37225583..37228610-chr14:37234821..37238583,4	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10134198	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10134532	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10134535	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1325533	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[ASN][1000 genomes]
rs1325534	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1325535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1325537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1739611	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1739613	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1749926	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1749927	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1749928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1749929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1749944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1853812	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2764953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2764954	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2764958	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2774037	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2774038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2774039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs712324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs712328	0.93[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs712333	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs73264788	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs848090	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs848093	0.91[CEU][hapmap]
rs848094	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs848095	0.89[EUR][1000 genomes]
rs848096	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs848098	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs848099	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs848100	0.89[EUR][1000 genomes]
rs848101	0.91[EUR][1000 genomes]
rs848102	0.89[EUR][1000 genomes]
rs848103	0.89[EUR][1000 genomes]
rs848104	0.90[EUR][1000 genomes]
rs848105	0.87[EUR][1000 genomes]
rs848108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs848109	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs848110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs848111	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs848113	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs848114	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs848115	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs848116	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs848118	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs848119	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs848122	0.93[CHB][hapmap]

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	nsv1047290	chr14:36564568-37445157	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1037952	chr14:36670484-37294692	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv542042	chr14:36670484-37294692	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1053685	chr14:36915643-37245920	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1749945	RP11-81F13.1	cis	Esophagus Mucosa	GTEx
rs1749945	RP11-81F13.2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:37217400-37234200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:37225800-37234000	Weak transcription	Esophagus	oesophagus
3	chr14:37227000-37227400	Enhancers	Fetal Thymus	thymus
4	chr14:37227000-37227600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
5	chr14:37227000-37227600	Enhancers	H1 Cell Line	embryonic stem cell
6	chr14:37227000-37227600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr14:37227000-37227600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr14:37227000-37227600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr14:37227000-37227600	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr14:37227000-37227600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr14:37227000-37227600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr14:37227000-37229000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr14:37227200-37227600	Enhancers	H9 Cell Line	embryonic stem cell
14	chr14:37227200-37227600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr14:37227200-37227800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr14:37227200-37228000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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