Variant report

Variant	rs9378676
Chromosome Location	chr6:2064264-2064265
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11242730	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11242734	0.83[CEU][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11242735	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11242740	0.80[GIH][hapmap]
rs11965306	0.83[GIH][hapmap]
rs12055694	0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12164011	0.82[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12528102	0.83[GIH][hapmap]
rs12530335	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12661847	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17134651	0.90[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4580917	0.82[CEU][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55635233	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56098578	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60898782	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62390706	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62390709	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62390733	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62392573	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs671240	0.94[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6920883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6921994	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6923662	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6924265	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6935616	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6935760	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7745086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7749136	0.82[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7753375	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7759455	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7768100	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9378319	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9378666	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9378667	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9378668	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9378670	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9378671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9378672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9378684	0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9391941	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9391943	1.00[CEU][hapmap];0.88[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9391944	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9392348	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs9392352	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9392353	0.82[CEU][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9392354	1.00[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9392356	0.85[CEU][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9392358	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9392365	0.83[AMR][1000 genomes]
rs9392368	0.83[AMR][1000 genomes]
rs9392371	0.82[JPT][hapmap]
rs9405539	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9405540	0.81[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9405541	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]
rs9405542	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9405546	0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9378676	WRNIP1	cis	parietal	SCAN
rs9378676	BPHL	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2022400-2080600	Weak transcription	Duodenum Mucosa	Duodenum
2	chr6:2056000-2080400	Weak transcription	HepG2	liver
3	chr6:2057600-2086400	Weak transcription	Aorta	Aorta
4	chr6:2059400-2080800	Weak transcription	Fetal Intestine Small	intestine
5	chr6:2062600-2086200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:2063200-2065000	Enhancers	Pancreas	Pancrea
7	chr6:2063800-2064400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:2063800-2065200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:2063800-2065200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:2064000-2064800	Enhancers	Brain Germinal Matrix	brain
11	chr6:2064000-2065200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:2064000-2065400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:2064200-2064800	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr6:2064200-2082600	Weak transcription	Stomach Mucosa	stomach
15	chr6:2064200-2094000	Weak transcription	Gastric	stomach

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