Variant report

Variant	rs4840160
Chromosome Location	chr6:101352914-101352915
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs11155708	0.83[ASN][1000 genomes]
rs11755579	0.88[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11758174	0.88[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11759127	1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12209186	0.83[ASN][1000 genomes]
rs13193416	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13205402	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13212730	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13220881	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337385	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1406894	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17672397	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17801075	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1813223	0.81[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1923013	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2004276	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2024842	0.82[AMR][1000 genomes]
rs2024843	0.89[ASN][1000 genomes]
rs2398247	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34555037	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34555727	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34716527	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34922716	0.84[AMR][1000 genomes]
rs35748724	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4240589	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4464803	0.94[ASN][1000 genomes]
rs4840156	0.82[AFR][1000 genomes]
rs4840157	0.86[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4840161	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4840164	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4840169	0.82[AMR][1000 genomes]
rs4840170	0.82[AMR][1000 genomes]
rs55967215	0.89[ASN][1000 genomes]
rs56359216	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs588204	0.92[ASN][1000 genomes]
rs599934	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs62419249	0.82[AMR][1000 genomes]
rs62420689	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62420692	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62422111	0.83[ASN][1000 genomes]
rs652335	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs669543	0.97[ASN][1000 genomes]
rs672437	0.82[ASN][1000 genomes]
rs679444	0.87[ASN][1000 genomes]
rs684140	0.92[ASN][1000 genomes]
rs6917195	0.83[ASN][1000 genomes]
rs694418	0.97[ASN][1000 genomes]
rs723742	0.83[CHB][hapmap]
rs7453078	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7740902	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7758630	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7772462	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9322270	1.00[ASW][hapmap];0.92[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9322271	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9322276	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9322279	0.97[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9377236	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9377240	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9377241	0.87[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9377251	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9386258	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9390698	1.00[ASW][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9390701	0.97[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9390702	0.97[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9399695	0.83[ASN][1000 genomes]
rs9399697	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9404059	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9404060	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9404069	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs979122	0.86[ASW][hapmap];0.82[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9791225	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs998254	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1020692	chr6:101136992-101426071	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886457	chr6:101158950-101487473	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1019213	chr6:101225650-101623140	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv538391	chr6:101225650-101623140	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv2763587	chr6:101277874-101510491	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv981366	chr6:101350432-101366644	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4840160	ASCC3	cis	cerebellum	SCAN
rs4840160	LIN28B	cis	parietal	SCAN
rs4840160	ASCC3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101351800-101353000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:101352000-101353200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr6:101352000-101353200	Enhancers	Placenta	Placenta
4	chr6:101352200-101353800	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr6:101352200-101354600	Enhancers	Dnd41	blood
6	chr6:101352400-101353200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:101352800-101353400	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr6:101352800-101354000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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