Variant report

Variant	rs12003902
Chromosome Location	chr9:16506261-16506262
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12345489	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs56679915	1.00[EUR][1000 genomes]
rs56873701	1.00[EUR][1000 genomes]
rs57014573	1.00[EUR][1000 genomes]
rs59485221	1.00[EUR][1000 genomes]
rs7025065	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7025366	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7025647	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7031782	0.90[EUR][1000 genomes]
rs7035471	1.00[EUR][1000 genomes]
rs7042044	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs73417433	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73645989	1.00[EUR][1000 genomes]
rs73645993	0.83[EUR][1000 genomes]
rs7854653	0.81[EUR][1000 genomes]
rs7858780	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7858802	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv892646	chr9:16476144-16514375	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS	lncRNA	n/a	inside rSNPs	diseases
6	nsv892647	chr9:16476144-16521534	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv466265	chr9:16484731-16516941	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	n/a	n/a	inside rSNPs	diseases
8	nsv613670	chr9:16484731-16516941	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16483200-16513600	Weak transcription	Psoas Muscle	Psoas
2	chr9:16495200-16509800	Weak transcription	Aorta	Aorta
3	chr9:16500000-16506400	Enhancers	HUVEC	blood vessel
4	chr9:16500200-16506600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:16500400-16514000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:16502200-16510000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:16502200-16510000	Weak transcription	HMEC	breast
8	chr9:16502400-16509800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:16503600-16506400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr9:16503800-16506600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:16504000-16506400	Enhancers	Hela-S3	cervix
12	chr9:16504000-16506400	Enhancers	NHLF	lung
13	chr9:16504000-16507000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:16504600-16506400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:16504600-16506600	Enhancers	Fetal Lung	lung
16	chr9:16505000-16506400	Enhancers	Fetal Kidney	kidney
17	chr9:16505000-16507000	Enhancers	Placenta	Placenta
18	chr9:16505200-16506400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr9:16505400-16506400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:16505400-16506400	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr9:16505400-16506600	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr9:16505400-16510000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:16505400-16510200	Weak transcription	NHEK	skin
24	chr9:16505400-16514000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr9:16505600-16506400	Enhancers	A549	lung
26	chr9:16505600-16506400	Enhancers	Osteobl	bone
27	chr9:16505600-16507000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:16505600-16509200	Weak transcription	Ovary	ovary
29	chr9:16505600-16510000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr9:16505600-16510000	Weak transcription	HSMMtube	muscle
31	chr9:16505800-16506400	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr9:16505800-16510000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr9:16506000-16506400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:16506000-16507000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr9:16506000-16509400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr9:16506000-16509400	Weak transcription	Colon Smooth Muscle	Colon
37	chr9:16506000-16509800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:16506000-16509800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr9:16506000-16509800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:16506000-16509800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr9:16506000-16509800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr9:16506000-16509800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr9:16506000-16510000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr9:16506000-16513600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr9:16506000-16514200	Weak transcription	NHDF-Ad	bronchial
46	chr9:16506000-16515200	Weak transcription	Adipose Nuclei	Adipose
47	chr9:16506200-16506400	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr9:16506200-16509600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:16506200-16509600	Weak transcription	Fetal Stomach	stomach
50	chr9:16506200-16509800	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links