Variant report

Variant	rs6511179
Chromosome Location	chr19:21197916-21197917
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 130 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10401931	1.00[CEU][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs10406661	0.92[CHD][hapmap];0.88[JPT][hapmap];0.92[MEX][hapmap]
rs10409844	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10409877	0.93[JPT][hapmap]
rs10410901	0.91[JPT][hapmap]
rs10412267	0.92[CHD][hapmap];0.88[JPT][hapmap];0.92[MEX][hapmap]
rs10412509	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs10412688	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10413175	0.90[EUR][1000 genomes]
rs10413692	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10417165	0.86[ASN][1000 genomes]
rs10418706	0.90[ASN][1000 genomes]
rs10422193	0.81[ASN][1000 genomes]
rs10423541	0.88[JPT][hapmap]
rs11085424	0.86[ASN][1000 genomes]
rs11085429	0.83[CEU][hapmap]
rs11085431	1.00[CEU][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs11666869	0.89[EUR][1000 genomes]
rs11668335	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11669248	0.87[EUR][1000 genomes]
rs11670162	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11671894	0.86[ASN][1000 genomes]
rs11672142	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11672727	0.88[JPT][hapmap]
rs11672747	0.88[JPT][hapmap]
rs12052091	0.83[CEU][hapmap]
rs12104387	0.91[ASN][1000 genomes]
rs12608706	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12608931	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12609167	1.00[ASW][hapmap];0.89[CEU][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];0.92[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12609427	0.89[EUR][1000 genomes]
rs12609510	0.86[ASN][1000 genomes]
rs12609831	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12611115	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12973640	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12975789	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12976796	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12981855	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1470021	0.88[JPT][hapmap]
rs1609441	0.88[JPT][hapmap]
rs1968523	1.00[CEU][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes]
rs1971054	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1975056	0.83[CEU][hapmap]
rs2081050	0.84[ASN][1000 genomes]
rs2081054	0.91[ASN][1000 genomes]
rs2081055	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2081056	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2081057	0.91[ASN][1000 genomes]
rs2098681	0.87[ASN][1000 genomes]
rs2099648	0.93[ASN][1000 genomes]
rs2112803	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2115493	0.88[JPT][hapmap]
rs2115494	0.88[JPT][hapmap]
rs2115495	0.92[CHD][hapmap];0.88[JPT][hapmap]
rs2115496	0.82[JPT][hapmap]
rs2164989	0.90[EUR][1000 genomes]
rs2195453	0.92[CHD][hapmap];0.88[JPT][hapmap]
rs2195454	0.88[JPT][hapmap]
rs2358792	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2358795	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2884548	0.91[ASN][1000 genomes]
rs2884554	1.00[CEU][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes]
rs4255903	0.91[ASN][1000 genomes]
rs4292035	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4365405	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4488591	0.88[JPT][hapmap]
rs4808273	0.81[ASN][1000 genomes]
rs4809119	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4809122	0.92[CHD][hapmap];0.88[JPT][hapmap];0.92[MEX][hapmap]
rs62122564	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62122565	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6511175	0.84[ASN][1000 genomes]
rs6511181	0.84[ASN][1000 genomes]
rs6511186	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6511187	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6511188	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6511191	1.00[CEU][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes]
rs6511192	0.88[JPT][hapmap]
rs6511194	0.87[JPT][hapmap]
rs6511195	0.93[JPT][hapmap]
rs6511196	0.87[JPT][hapmap]
rs7246723	0.88[JPT][hapmap]
rs7247413	0.86[ASN][1000 genomes]
rs7247553	0.93[ASN][1000 genomes]
rs7248087	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7249283	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7249736	1.00[CEU][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes]
rs7252277	0.86[ASN][1000 genomes]
rs7253530	0.86[ASN][1000 genomes]
rs7254047	0.88[JPT][hapmap]
rs7254053	0.93[JPT][hapmap]
rs7254722	0.83[ASN][1000 genomes]
rs7254768	0.93[ASN][1000 genomes]
rs7257481	0.89[EUR][1000 genomes]
rs7258195	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7258409	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7258477	0.91[ASN][1000 genomes]
rs7258831	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7259653	0.91[ASN][1000 genomes]
rs7260268	0.87[CHD][hapmap];0.88[JPT][hapmap]
rs7260600	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7343175	0.89[EUR][1000 genomes]
rs8100289	0.86[EUR][1000 genomes]
rs8101412	0.90[EUR][1000 genomes]
rs8101461	0.89[EUR][1000 genomes]
rs8102966	0.91[ASN][1000 genomes]
rs8103696	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8106801	0.92[CHD][hapmap];0.87[JPT][hapmap]
rs8106923	0.88[JPT][hapmap]
rs8107638	1.00[CEU][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes]
rs8107982	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8109549	0.89[EUR][1000 genomes]
rs8109577	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8111827	0.92[CHD][hapmap];0.88[JPT][hapmap];0.92[MEX][hapmap]
rs8112054	0.92[CHD][hapmap];0.88[JPT][hapmap]
rs8112216	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.89[LWK][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8113541	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs8182465	0.93[JPT][hapmap]
rs9304980	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9304981	0.81[JPT][hapmap]
rs9304982	0.92[CHD][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap]
rs9941463	0.86[ASN][1000 genomes]

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	nsv1062776	chr19:20818886-21273361	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS 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	32 gene(s)	inside rSNPs	diseases
2	nsv932110	chr19:20818886-21278952	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers 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	32 gene(s)	inside rSNPs	diseases
3	esv2763043	chr19:20818886-21290543	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers 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	32 gene(s)	inside rSNPs	diseases
5	nsv817536	chr19:21041855-21348237	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	esv1850387	chr19:21109758-21294264	Active TSS ZNF genes & repeats Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv911411	chr19:21184533-21263518	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv578949	chr19:21190572-21244049	ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6511179	ZNF714	cis	parietal	SCAN
rs6511179	ZNF429	cis	cerebellum	SCAN
rs6511179	ZNF429	cis	parietal	SCAN
rs6511179	RFXANK	cis	cerebellum	SCAN
rs6511179	MYO9B	cis	cerebellum	SCAN
rs6511179	ZNF714	cis	cerebellum	SCAN
rs6511179	ZNF100	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21184000-21198000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr19:21192200-21203000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr19:21192400-21203000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr19:21192400-21203400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:21192600-21203000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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