Variant report

Variant	rs7247982
Chromosome Location	chr19:53719115-53719116
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53705415..53707075-chr19:53718366..53721132,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VN1R2-5	chr19:53716201-53719355	NONHSAT067648

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10401578	0.87[CHB][hapmap]
rs10404048	0.81[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs10413453	0.88[ASN][1000 genomes]
rs10417666	0.81[ASN][1000 genomes]
rs10775558	0.82[CHB][hapmap]
rs10853859	0.82[CHB][hapmap]
rs11084227	0.87[CHB][hapmap]
rs1129002	0.87[CHB][hapmap]
rs12981894	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12984188	0.87[CHB][hapmap]
rs12984473	0.87[CHB][hapmap]
rs17272966	0.87[CHB][hapmap]
rs2914371	0.82[CHB][hapmap]
rs2914372	0.80[CHB][hapmap]
rs2914376	0.87[CHB][hapmap]
rs2914378	0.87[CHB][hapmap]
rs2914381	1.00[CHB][hapmap]
rs2914383	0.82[CHB][hapmap]
rs2965221	1.00[CHB][hapmap]
rs2965223	1.00[CHB][hapmap]
rs2965224	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs2965228	0.81[ASW][hapmap]
rs2965230	1.00[CHB][hapmap]
rs2965231	1.00[CHB][hapmap]
rs2965242	0.80[CHB][hapmap]
rs4239497	0.90[ASN][1000 genomes]
rs4447544	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4801965	0.80[CHB][hapmap]
rs4801970	0.82[CHB][hapmap]
rs4801972	0.82[ASN][1000 genomes]
rs4803062	0.84[ASN][1000 genomes]
rs4803063	0.84[ASN][1000 genomes]
rs4803068	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4803070	0.85[ASN][1000 genomes]
rs55852652	0.81[ASN][1000 genomes]
rs6509734	0.81[ASN][1000 genomes]
rs6509736	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248781	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7248812	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7249771	0.84[ASN][1000 genomes]
rs7249931	0.83[ASN][1000 genomes]
rs7253646	0.82[ASN][1000 genomes]
rs8101908	0.82[ASN][1000 genomes]
rs8102940	0.80[ASN][1000 genomes]
rs8109793	0.82[ASN][1000 genomes]
rs9788	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv912342	chr19:53581151-54010759	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1063630	chr19:53591444-54419183	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	282 gene(s)	inside rSNPs	diseases
7	nsv1055378	chr19:53603268-53951855	Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv544065	chr19:53603268-53951855	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	esv2830362	chr19:53681132-53933147	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7247982	ISOC2	cis	cerebellum	SCAN
rs7247982	PRPF31	cis	parietal	SCAN
rs7247982	ZNF17	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53701600-53720200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
2	chr19:53701600-53724800	ZNF genes & repeats	Liver	Liver
3	chr19:53701600-53725000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr19:53701600-53725000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
5	chr19:53701800-53725400	ZNF genes & repeats	Adipose Nuclei	Adipose
6	chr19:53702400-53724800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:53711200-53720200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
8	chr19:53712400-53720200	ZNF genes & repeats	Brain Anterior Caudate	brain
9	chr19:53718400-53720800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
10	chr19:53719000-53720000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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