Variant report

Variant	rs9405541
Chromosome Location	chr6:2052811-2052812
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11242730	0.87[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11242734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11242735	0.97[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11242740	0.80[GIH][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap]
rs11965306	0.83[GIH][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap]
rs12055694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12164011	0.81[JPT][hapmap]
rs12528102	0.83[GIH][hapmap];0.87[JPT][hapmap]
rs12530335	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661847	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17134651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17134732	0.80[CEU][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap]
rs3778557	0.87[JPT][hapmap]
rs3800178	0.81[JPT][hapmap]
rs4580917	0.82[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.90[ASN][1000 genomes]
rs55635233	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60898782	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62390706	0.84[ASN][1000 genomes]
rs62390709	0.80[ASN][1000 genomes]
rs62390733	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62392573	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6920883	0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6921994	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6923662	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6924265	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6935616	0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6935760	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7745086	0.82[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7749136	0.93[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs7753375	0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7759455	0.90[ASN][1000 genomes]
rs7768100	0.81[AMR][1000 genomes]
rs9378319	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9378666	0.84[ASN][1000 genomes]
rs9378667	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9378668	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9378670	0.82[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9378671	0.87[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9378672	0.97[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9378676	0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9378684	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9378685	0.87[JPT][hapmap]
rs9391941	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9391943	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9391944	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9392348	0.93[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs9392352	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9392353	0.87[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.92[ASN][1000 genomes]
rs9392354	0.90[CHD][hapmap];0.88[MEX][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9392356	0.82[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.90[ASN][1000 genomes]
rs9392358	1.00[CEU][hapmap];0.88[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9392365	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9392368	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9392371	0.80[JPT][hapmap];0.80[AMR][1000 genomes]
rs9405157	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs9405539	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9405540	0.93[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs9405542	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9405546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	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
4	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
5	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
6	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
7	nsv981098	chr6:2008599-2102267	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv527735	chr6:2028237-2097654	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv522608	chr6:2032259-2203888	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1019227	chr6:2038843-2142395	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv538097	chr6:2038843-2142395	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2022400-2055600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:2022400-2080600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:2030000-2053600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:2051600-2058200	Weak transcription	Fetal Intestine Small	intestine
5	chr6:2052600-2053200	Strong transcription	HepG2	liver
6	chr6:2052800-2053200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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