Variant report

Variant	rs9392348
Chromosome Location	chr6:1989604-1989605
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11242730	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs11242734	0.84[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs11242735	1.00[CEU][hapmap]
rs11242740	0.92[JPT][hapmap]
rs11965306	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs12055694	0.93[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12164011	0.91[CEU][hapmap];0.81[JPT][hapmap]
rs12530335	1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[ASN][1000 genomes]
rs12661847	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17134651	0.93[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs17134732	0.92[JPT][hapmap]
rs3778557	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs4580917	0.90[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs55635233	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62390706	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62390733	0.80[EUR][1000 genomes]
rs6920883	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6935616	1.00[CEU][hapmap]
rs6935760	0.80[EUR][1000 genomes]
rs7745086	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7749136	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs7753375	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7759455	0.84[ASN][1000 genomes]
rs9378666	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9378667	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9378668	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9378670	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs9378671	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs9378672	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs9378676	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs9378684	0.94[CHB][hapmap]
rs9378685	0.93[JPT][hapmap]
rs9391941	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9391943	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9391944	0.81[EUR][1000 genomes]
rs9392352	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9392353	0.90[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs9392354	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs9392356	0.95[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs9405157	0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs9405539	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9405540	0.90[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs9405541	0.93[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs9405542	0.83[ASN][1000 genomes]
rs9405546	0.93[CHB][hapmap];0.82[JPT][hapmap]

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	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
5	nsv1032149	chr6:1848148-2006021	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1032727	chr6:1900622-2064690	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv538095	chr6:1900622-2064690	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv883386	chr6:1910108-2122454	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1972000-1992200	Weak transcription	Gastric	stomach
2	chr6:1979000-1991600	Weak transcription	Fetal Stomach	stomach
3	chr6:1985000-2010200	Weak transcription	Fetal Intestine Large	intestine
4	chr6:1987400-2003600	Weak transcription	Aorta	Aorta
5	chr6:1987800-1992800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:1988400-1992600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:1988400-1992800	Weak transcription	Osteobl	bone
8	chr6:1988400-1993200	Weak transcription	NH-A	brain
9	chr6:1988400-1993400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:1988400-1993400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:1988400-2008600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:1988600-1993000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:1988600-1993000	Weak transcription	NHEK	skin
14	chr6:1988800-1992800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:1988800-1993000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:1988800-1993200	Weak transcription	HMEC	breast
17	chr6:1988800-1995400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:1989000-1990200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:1989200-1990200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr6:1989200-1990200	Enhancers	Pancreas	Pancrea
21	chr6:1989400-1990000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:1989400-1990200	Enhancers	HepG2	liver
23	chr6:1989600-1992000	Weak transcription	Fetal Intestine Small	intestine

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