Variant report

Variant	rs7853728
Chromosome Location	chr9:3439919-3439920
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10115757	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10115791	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10117431	0.80[CHB][hapmap]
rs10117846	1.00[JPT][hapmap]
rs10124292	0.89[CHB][hapmap]
rs10124295	1.00[CHB][hapmap]
rs10814096	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10814097	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10971667	0.80[CHB][hapmap]
rs10971685	0.89[JPT][hapmap]
rs10971976	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10972042	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs10972061	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10972079	0.84[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs12115798	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12337095	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12339955	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12340535	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs12341652	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs12341737	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs12346432	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs12554323	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs13286511	0.89[CHB][hapmap]
rs13290412	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs13295925	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13297034	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13298219	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs13298908	0.90[JPT][hapmap]
rs13300358	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13300995	0.85[ASN][1000 genomes]
rs13301035	0.90[ASN][1000 genomes]
rs13302664	0.80[CHB][hapmap]
rs13302841	0.84[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs16924266	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1998976	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs2380762	0.89[EUR][1000 genomes]
rs34086781	0.82[ASN][1000 genomes]
rs34708788	0.82[ASN][1000 genomes]
rs34770513	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35412653	0.87[ASN][1000 genomes]
rs36091570	0.90[ASN][1000 genomes]
rs3758195	0.88[JPT][hapmap]
rs3758196	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs4741829	0.90[JPT][hapmap]
rs57004251	0.82[ASN][1000 genomes]
rs6476436	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6476451	0.84[ASN][1000 genomes]
rs7022711	0.81[JPT][hapmap]
rs7024933	0.90[JPT][hapmap]
rs7028812	0.89[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs7030212	0.81[ASN][1000 genomes]
rs7040113	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7041836	0.89[JPT][hapmap]
rs7043493	0.80[CHB][hapmap]
rs71506643	0.82[EUR][1000 genomes]
rs71506645	0.82[ASN][1000 genomes]
rs7850576	0.83[EUR][1000 genomes]
rs7854273	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7864440	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7864459	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9695619	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv1034280	chr9:3319718-3491987	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv539942	chr9:3319718-3491987	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv613147	chr9:3368111-3440355	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv892090	chr9:3391364-3496660	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1019324	chr9:3436845-3502815	ZNF genes & repeats Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1022795	chr9:3436845-3744623	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 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	chr9:3425600-3453200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr9:3426600-3444600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:3426800-3446200	Weak transcription	Left Ventricle	heart
4	chr9:3428200-3443200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:3429800-3443800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:3431800-3441400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr9:3432400-3467800	Weak transcription	GM12878-XiMat	blood
8	chr9:3432600-3460600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr9:3435000-3473200	Weak transcription	Primary T cells from cord blood	blood
10	chr9:3435800-3444000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr9:3437800-3446000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr9:3438400-3443200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:3438400-3472800	Weak transcription	Primary B cells from cord blood	blood

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