Variant report

Variant	rs16917215
Chromosome Location	chr9:3343404-3343405
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12337888	1.00[GIH][hapmap]
rs13283906	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13286357	0.85[EUR][1000 genomes]
rs13288291	0.85[EUR][1000 genomes]
rs13299535	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs16916086	0.82[YRI][hapmap]
rs16916097	0.82[YRI][hapmap]
rs16916457	0.80[YRI][hapmap]
rs17658908	1.00[CEU][hapmap]
rs17659039	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs17715422	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs34354121	0.94[EUR][1000 genomes]
rs34885235	0.85[EUR][1000 genomes]
rs35110056	0.89[EUR][1000 genomes]
rs35639292	0.83[EUR][1000 genomes]
rs36086495	0.89[EUR][1000 genomes]
rs6476405	0.82[YRI][hapmap]
rs7042345	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs7863972	0.89[CEU][hapmap];1.00[GIH][hapmap];0.96[EUR][1000 genomes]
rs7870506	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892086	chr9:3012276-3410838	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv466090	chr9:3237378-3349487	Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv613145	chr9:3237378-3349487	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3288200-3378400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr9:3293600-3352600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:3309400-3350400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:3313400-3352400	Weak transcription	Primary T cells from cord blood	blood
5	chr9:3319000-3347800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr9:3319800-3353800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr9:3320600-3347200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr9:3322600-3348800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr9:3328400-3344400	Weak transcription	Fetal Lung	lung
10	chr9:3330400-3354200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr9:3331000-3343600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:3333000-3352600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr9:3337800-3352600	Weak transcription	Primary B cells from cord blood	blood
14	chr9:3337800-3388800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr9:3338800-3347000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:3338800-3348200	Weak transcription	Brain Anterior Caudate	brain
17	chr9:3341200-3397600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr9:3341600-3344200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:3341600-3344200	Enhancers	NHDF-Ad	bronchial
20	chr9:3341600-3346200	Weak transcription	GM12878-XiMat	blood
21	chr9:3341800-3343800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:3341800-3344200	Enhancers	Osteobl	bone
23	chr9:3341800-3345200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr9:3342000-3343800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:3342000-3344600	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr9:3343000-3345200	Enhancers	HepG2	liver
27	chr9:3343200-3344000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links