Variant report

Variant	rs12380363
Chromosome Location	chr9:117885635-117885636
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1000109	0.95[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1000110	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1000111	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10759756	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10759757	0.95[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10817714	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10817715	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10817716	0.95[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10817718	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10982550	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10982557	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10982572	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10982576	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs10982598	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1111784	0.95[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11788578	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11792657	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11793679	0.95[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11794627	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12376564	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12376870	0.94[ASN][1000 genomes]
rs12378459	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12379019	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12554357	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12554651	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1335350	0.88[CHB][hapmap]
rs1360290	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1411458	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1414146	0.88[CHB][hapmap]
rs16936516	0.95[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2001693	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2012566	0.95[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2012775	0.95[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2900594	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3748166	0.87[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4448357	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4978620	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4978627	0.85[TSI][hapmap]
rs4979500	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4979501	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4979503	0.91[CEU][hapmap]
rs4979506	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs57814325	0.94[ASN][1000 genomes]
rs58134557	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58160054	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61508829	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62580502	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6478132	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7018653	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7021057	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7024048	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7025283	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7029482	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7029844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7035705	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7039636	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7039915	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7040243	0.88[CHB][hapmap]
rs7040521	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7849460	0.95[CEU][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7849467	0.95[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7850000	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7850007	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7851185	0.88[CHB][hapmap];0.85[TSI][hapmap]
rs7858535	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7865971	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7866695	0.85[TSI][hapmap]
rs884790	0.90[AMR][1000 genomes];0.94[EUR][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	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893768	chr9:117853103-117903975	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117881400-117886000	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr9:117882000-117888800	Weak transcription	NHLF	lung
3	chr9:117883600-117888600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:117884000-117887200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:117884000-117888800	Weak transcription	Fetal Muscle Leg	muscle
6	chr9:117884000-117892600	Weak transcription	Colon Smooth Muscle	Colon
7	chr9:117884200-117888800	Weak transcription	Osteobl	bone
8	chr9:117884400-117887600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:117884800-117886000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
10	chr9:117885200-117885800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:117885400-117885800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:117885400-117885800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:117885600-117885800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell

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