Variant report

Variant	rs7259197
Chromosome Location	chr19:39542089-39542090
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:39542060-39542210	GM12873	blood:	n/a	n/a
2	CTCF	chr19:39541880-39542170	HRPEpiC	eye:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39536592..39538414-chr19:39541757..39543284,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251709	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10406222	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10416823	0.88[ASN][1000 genomes]
rs10417436	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.88[ASN][1000 genomes]
rs10424827	0.89[ASN][1000 genomes]
rs10426645	0.87[ASN][1000 genomes]
rs10426661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10853724	0.88[ASN][1000 genomes]
rs11083499	0.85[ASN][1000 genomes]
rs11083500	0.87[ASN][1000 genomes]
rs11083501	0.88[ASN][1000 genomes]
rs11083502	1.00[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.87[ASN][1000 genomes]
rs11667641	1.00[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.86[ASN][1000 genomes]
rs11670486	0.87[ASN][1000 genomes]
rs11670520	0.84[ASN][1000 genomes]
rs11880441	0.88[ASN][1000 genomes]
rs11883422	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs12609806	0.91[CHB][hapmap];0.84[GIH][hapmap];0.85[ASN][1000 genomes]
rs12971842	0.83[ASN][1000 genomes]
rs12972850	0.86[ASN][1000 genomes]
rs12972978	0.86[ASN][1000 genomes]
rs12978749	0.85[ASN][1000 genomes]
rs12982349	0.81[ASN][1000 genomes]
rs12982529	0.83[ASN][1000 genomes]
rs12985447	0.83[ASN][1000 genomes]
rs1651748	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1840745	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.88[ASN][1000 genomes]
rs1840746	0.86[ASN][1000 genomes]
rs1840747	0.86[ASN][1000 genomes]
rs1840748	1.00[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.87[ASN][1000 genomes]
rs1864191	0.87[ASN][1000 genomes]
rs1869983	0.90[ASN][1000 genomes]
rs36154890	0.88[ASN][1000 genomes]
rs3848623	0.86[ASN][1000 genomes]
rs4280369	0.88[ASN][1000 genomes]
rs4803185	0.88[ASN][1000 genomes]
rs4803186	0.88[ASN][1000 genomes]
rs4803187	0.88[ASN][1000 genomes]
rs4803188	0.89[ASN][1000 genomes]
rs4803193	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.90[ASN][1000 genomes]
rs58897626	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60775146	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62119538	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs628335	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6508838	0.81[ASN][1000 genomes]
rs6508839	0.83[ASN][1000 genomes]
rs6508840	0.83[ASN][1000 genomes]
rs6508841	0.95[CHB][hapmap];0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs6508842	0.88[ASN][1000 genomes]
rs6508843	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs681496	0.87[ASN][1000 genomes]
rs7247801	0.88[ASN][1000 genomes]
rs7248513	0.88[ASN][1000 genomes]
rs7248652	0.88[ASN][1000 genomes]
rs7250110	0.85[ASN][1000 genomes]
rs7250431	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.90[ASN][1000 genomes]
rs7251264	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs7255211	0.83[ASN][1000 genomes]
rs7256126	0.81[ASN][1000 genomes]
rs7258862	0.89[ASN][1000 genomes]
rs7259064	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259801	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.86[ASN][1000 genomes]
rs8104751	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.88[ASN][1000 genomes]
rs8104899	0.88[ASN][1000 genomes]
rs8104990	0.88[ASN][1000 genomes]
rs8105865	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963126	chr19:39521120-39552490	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2760517	chr19:39530012-39544234	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7259197	GLTSCR1	cis	cerebellum	SCAN
rs7259197	ZNF155	cis	parietal	SCAN
rs7259197	CTB-189B5.3	cis	Skin Sun Exposed Lower leg	GTEx
rs7259197	FBXO27	cis	Esophagus Mucosa	GTEx
rs7259197	CTB-189B5.3	cis	Esophagus Mucosa	GTEx
rs7259197	ZFP112	cis	parietal	SCAN
rs7259197	ATP5SL	cis	cerebellum	SCAN
rs7259197	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39530800-39543000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr19:39537600-39543000	Weak transcription	A549	lung
3	chr19:39538800-39542200	Weak transcription	Fetal Intestine Large	intestine
4	chr19:39538800-39543000	Weak transcription	Fetal Intestine Small	intestine
5	chr19:39541200-39546400	Weak transcription	Right Atrium	heart
6	chr19:39541800-39542400	Enhancers	HepG2	liver
7	chr19:39541800-39543200	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr19:39542000-39542200	Enhancers	Brain Hippocampus Middle	brain

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