Variant report

Variant	rs12339625
Chromosome Location	chr9:16570779-16570780
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10116857	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10118895	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10120002	0.80[EUR][1000 genomes]
rs10120281	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10122372	0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10123515	0.92[EUR][1000 genomes]
rs10124530	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10125014	1.00[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs10733311	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs10733312	0.86[AMR][1000 genomes]
rs10738437	0.85[ASW][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes]
rs10738440	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10756764	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10756765	1.00[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap]
rs10962484	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10962510	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12000426	1.00[CEU][hapmap]
rs12004304	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12337676	0.89[AMR][1000 genomes]
rs12340504	0.86[EUR][1000 genomes]
rs12350242	0.84[EUR][1000 genomes]
rs12352543	0.84[YRI][hapmap]
rs1337393	0.89[AMR][1000 genomes]
rs1337400	0.85[AMR][1000 genomes]
rs1415475	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1415476	0.85[MEX][hapmap];0.85[AMR][1000 genomes]
rs1538102	0.83[EUR][1000 genomes]
rs16934816	1.00[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16934842	0.84[EUR][1000 genomes]
rs16934855	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs16934875	1.00[GIH][hapmap];0.91[TSI][hapmap]
rs16934886	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17738890	0.97[EUR][1000 genomes]
rs1927626	0.85[AMR][1000 genomes]
rs2095657	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2149159	0.82[EUR][1000 genomes]
rs28428651	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28457730	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28490464	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28501274	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28648047	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28651010	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4466493	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4961725	1.00[CEU][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56218971	0.97[EUR][1000 genomes]
rs59379949	0.88[EUR][1000 genomes]
rs7018743	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7018877	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7019016	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7019105	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7019625	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7032239	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7032523	1.00[CEU][hapmap]
rs7032772	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7035303	0.81[AMR][1000 genomes]
rs7036282	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7048399	0.85[AMR][1000 genomes]
rs7048805	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs725011	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73417477	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7470623	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7854979	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7859395	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7859971	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7862214	0.80[EUR][1000 genomes]
rs7870380	0.81[EUR][1000 genomes]
rs7870508	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7870730	1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7873338	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv528443	chr9:16570142-16581967	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16552800-16571000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr9:16552800-16571400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:16553000-16575200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:16556400-16575600	Weak transcription	HSMM	muscle
5	chr9:16560200-16571200	Weak transcription	Ovary	ovary
6	chr9:16560200-16571400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:16560200-16571600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:16566600-16573000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr9:16568800-16575200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr9:16569600-16572200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr9:16569600-16572400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr9:16569600-16572400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr9:16569800-16572000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr9:16569800-16572400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr9:16569800-16582400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:16570000-16571200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr9:16570000-16572200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:16570400-16570800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:16570400-16570800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:16570400-16570800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr9:16570400-16570800	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr9:16570400-16571000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:16570400-16571400	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr9:16570400-16572400	Enhancers	Colon Smooth Muscle	Colon
25	chr9:16570600-16571000	Active TSS	Fetal Lung	lung
26	chr9:16570600-16571200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:16570600-16571200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr9:16570600-16571400	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr9:16570600-16571400	Enhancers	A549	lung
30	chr9:16570600-16571600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr9:16570600-16571800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:16570600-16572200	Enhancers	Primary hematopoietic stem cells	blood
33	chr9:16570600-16572200	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr9:16570600-16572600	Enhancers	Osteobl	bone
35	chr9:16570600-16572800	Enhancers	NHLF	lung
36	chr9:16570600-16573000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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