Variant report

Variant	rs10962599
Chromosome Location	chr9:16795286-16795287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10756812	0.84[ASW][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.86[AFR][1000 genomes]
rs10810619	0.81[GIH][hapmap]
rs10810636	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10810638	1.00[LWK][hapmap]
rs10962582	0.84[GIH][hapmap]
rs10962590	0.86[AFR][1000 genomes]
rs10962596	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10962597	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10962600	0.94[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10962605	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10962612	0.89[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11789463	1.00[LWK][hapmap]
rs11795031	0.84[ASW][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.86[AFR][1000 genomes]
rs12345910	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12375569	0.95[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2026804	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2026805	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2254330	0.89[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4433240	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4448381	1.00[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2758627	chr9:16641966-16809203	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2759673	chr9:16641966-16809203	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription 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	10 gene(s)	inside rSNPs	diseases
5	nsv892650	chr9:16696187-16950860	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv613671	chr9:16792350-16804082	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10962599	KIAA1797	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16767600-16795400	Weak transcription	Fetal Muscle Leg	muscle
2	chr9:16769800-16795400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:16784400-16802200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:16786000-16795600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:16787200-16797600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:16788200-16798000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr9:16792400-16796200	Enhancers	Colon Smooth Muscle	Colon
8	chr9:16794000-16795600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:16794000-16796600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:16794200-16796200	Enhancers	H1 Cell Line	embryonic stem cell
11	chr9:16794200-16796200	Enhancers	Ovary	ovary
12	chr9:16794200-16796600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr9:16794400-16795400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr9:16794600-16795400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:16794600-16795800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:16794600-16796600	Enhancers	Osteobl	bone
17	chr9:16794600-16797000	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr9:16794600-16799000	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr9:16794600-16799200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr9:16794800-16795800	Enhancers	Fetal Lung	lung
21	chr9:16794800-16796200	Enhancers	H9 Cell Line	embryonic stem cell
22	chr9:16794800-16796200	Enhancers	HSMM	muscle
23	chr9:16794800-16796200	Flanking Active TSS	NHDF-Ad	bronchial
24	chr9:16794800-16799000	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr9:16794800-16799800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:16795000-16795400	Enhancers	NH-A	brain
27	chr9:16795000-16795600	Enhancers	HSMMtube	muscle
28	chr9:16795000-16796000	Enhancers	HUVEC	blood vessel
29	chr9:16795000-16796200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr9:16795000-16796200	Enhancers	Fetal Stomach	stomach
31	chr9:16795000-16796400	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr9:16795000-16796400	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr9:16795000-16796600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr9:16795000-16798000	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr9:16795000-16799200	Enhancers	Rectal Smooth Muscle	rectum
36	chr9:16795200-16795600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr9:16795200-16795600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr9:16795200-16795600	Weak transcription	NHLF	lung
39	chr9:16795200-16796000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:16795200-16796000	Enhancers	Adipose Nuclei	Adipose
41	chr9:16795200-16796200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr9:16795200-16798000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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