Variant report

Variant	rs3853431
Chromosome Location	chr9:15272308-15272309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10121394	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10961941	0.86[JPT][hapmap]
rs10961946	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10961948	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10961951	0.88[ASW][hapmap];0.85[CEU][hapmap];0.88[CHB][hapmap];0.92[LWK][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12005971	0.86[JPT][hapmap]
rs12336514	0.86[JPT][hapmap]
rs12338912	0.86[JPT][hapmap]
rs12349572	0.94[ASW][hapmap];0.85[CEU][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12349889	0.85[EUR][1000 genomes]
rs12352604	0.86[JPT][hapmap]
rs3853430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3853432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3901749	1.00[ASW][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7023109	1.00[JPT][hapmap]
rs7030770	0.85[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7048177	1.00[JPT][hapmap]
rs7846987	0.86[JPT][hapmap]
rs7855226	0.85[CEU][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7862248	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7862255	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7864179	0.86[JPT][hapmap]
rs7870745	1.00[JPT][hapmap]
rs7873299	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7873760	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874222	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874421	1.00[JPT][hapmap]
rs912280	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031340	chr9:15163004-15332769	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer 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:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15238400-15275400	Weak transcription	Fetal Intestine Large	intestine
2	chr9:15240600-15275400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr9:15241200-15273400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr9:15241200-15286200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr9:15243000-15293400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr9:15244600-15273400	Weak transcription	Stomach Mucosa	stomach
7	chr9:15249600-15276200	Weak transcription	Fetal Kidney	kidney
8	chr9:15249800-15276200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:15250200-15288200	Weak transcription	Fetal Stomach	stomach
10	chr9:15251400-15273600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr9:15253600-15272800	Weak transcription	Gastric	stomach
12	chr9:15253800-15286400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr9:15254000-15293000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:15254200-15275400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr9:15254200-15276600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr9:15254200-15293000	Weak transcription	NHEK	skin
17	chr9:15254200-15295600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:15257000-15277800	Weak transcription	Fetal Lung	lung
19	chr9:15257200-15273600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:15257400-15275200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:15259200-15293400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr9:15260600-15283000	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:15261800-15279200	Weak transcription	Ovary	ovary
24	chr9:15263000-15276200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr9:15263800-15283000	Weak transcription	Aorta	Aorta
26	chr9:15264200-15285800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr9:15266000-15273600	Weak transcription	HepG2	liver
28	chr9:15268600-15273400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:15268800-15277400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:15269000-15274000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr9:15269200-15273000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr9:15271400-15273600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr9:15271600-15273800	Strong transcription	Fetal Intestine Small	intestine
34	chr9:15271600-15274600	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr9:15272000-15272400	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr9:15272000-15272800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr9:15272000-15273600	Strong transcription	Primary T cells from cord blood	blood
38	chr9:15272000-15274400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr9:15272200-15273000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr9:15272200-15273800	Enhancers	Lung	lung
41	chr9:15272200-15276200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr9:15272200-15276400	Weak transcription	Left Ventricle	heart

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