Variant report

Variant	rs4979499
Chromosome Location	chr9:117899652-117899653
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1000109	0.82[CEU][hapmap]
rs10759756	0.83[CEU][hapmap]
rs10759757	0.82[CEU][hapmap]
rs10817716	0.82[CEU][hapmap]
rs10817718	0.82[CEU][hapmap];0.87[ASN][1000 genomes]
rs10982557	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10982572	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10982576	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10982598	0.84[ASN][1000 genomes]
rs1111784	0.82[CEU][hapmap]
rs11788578	0.87[CEU][hapmap]
rs11792657	0.83[CEU][hapmap]
rs11793679	0.82[CEU][hapmap]
rs11794627	0.86[ASN][1000 genomes]
rs12376870	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12380363	0.90[ASN][1000 genomes]
rs1360290	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1414146	0.86[CEU][hapmap]
rs16936516	0.82[CEU][hapmap]
rs2001693	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2012566	0.82[CEU][hapmap]
rs2012775	0.82[CEU][hapmap]
rs4448357	0.85[ASN][1000 genomes]
rs4587405	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4979500	0.83[CEU][hapmap]
rs4979501	0.83[CEU][hapmap]
rs4979506	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57814325	0.88[ASN][1000 genomes]
rs7025283	0.94[ASN][1000 genomes]
rs7029482	0.84[ASN][1000 genomes]
rs7029844	0.83[CEU][hapmap];0.88[ASN][1000 genomes]
rs7040243	0.86[CEU][hapmap]
rs7040521	0.83[CEU][hapmap]
rs7849460	0.82[CEU][hapmap]
rs7849467	0.82[CEU][hapmap]
rs7850000	0.83[CEU][hapmap];0.94[ASN][1000 genomes]
rs7850007	0.83[CEU][hapmap]
rs7865971	0.83[CEU][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv6681	chr9:117893926-117938609	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117890200-117909000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:117895400-117900000	Enhancers	NHLF	lung
3	chr9:117895400-117903200	Weak transcription	Fetal Kidney	kidney
4	chr9:117896200-117899800	Enhancers	Colon Smooth Muscle	Colon
5	chr9:117896600-117900400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:117896800-117900200	Enhancers	Fetal Lung	lung
7	chr9:117897800-117905000	Weak transcription	Osteobl	bone
8	chr9:117898200-117900000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr9:117898400-117905000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:117898600-117899800	Weak transcription	Spleen	Spleen
11	chr9:117898800-117900000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:117898800-117900200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:117899200-117899800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr9:117899200-117900800	Enhancers	Fetal Intestine Large	intestine
15	chr9:117899200-117900800	Enhancers	Fetal Intestine Small	intestine
16	chr9:117899400-117900600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:117899600-117900000	Enhancers	Fetal Heart	heart
18	chr9:117899600-117900200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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