Variant report

Variant	rs349046
Chromosome Location	chr19:44300626-44300627
allele	C/T
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	chr19:44300600-44300750	WI-38	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000268601	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10401170	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10401203	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405457	0.81[ASN][1000 genomes]
rs10421887	0.81[ASN][1000 genomes]
rs10422990	0.81[ASN][1000 genomes]
rs10426528	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11665924	0.92[CHB][hapmap];0.90[CHD][hapmap]
rs12460161	0.81[ASN][1000 genomes]
rs12974061	0.81[ASN][1000 genomes]
rs349045	0.89[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs349047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs349048	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs349049	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs349050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs349053	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs349055	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3760982	0.92[CHB][hapmap];0.90[CHD][hapmap]
rs3760983	0.92[CHB][hapmap];0.90[CHD][hapmap]
rs56103707	0.92[ASN][1000 genomes]
rs56344893	0.81[ASN][1000 genomes]
rs56681946	0.81[ASN][1000 genomes]
rs60184524	0.81[ASN][1000 genomes]
rs62116990	0.97[ASN][1000 genomes]
rs62116991	0.92[ASN][1000 genomes]
rs73048670	0.81[ASN][1000 genomes]
rs8104447	1.00[ASN][1000 genomes]
rs8111664	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs349046	ZNF296	cis	parietal	SCAN
rs349046	AC115522.3	cis	Skin Sun Exposed Lower leg	GTEx
rs349046	ZNF404	trans	parietal	SCAN
rs349046	CD3EAP	cis	cerebellum	SCAN
rs349046	GEMIN7	cis	cerebellum	SCAN
rs349046	LRRC4B	cis	parietal	SCAN
rs349046	KCNN4	cis	Whole Blood	GTEx
rs349046	ZNF296	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44289400-44302600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:44289800-44300800	Weak transcription	Placenta	Placenta
3	chr19:44290000-44302400	Weak transcription	NHEK	skin
4	chr19:44290200-44302200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr19:44299000-44302000	Weak transcription	Brain Angular Gyrus	brain
6	chr19:44299600-44301400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr19:44299600-44302200	Weak transcription	Brain Anterior Caudate	brain
8	chr19:44299600-44302400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr19:44300000-44301000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:44300200-44301800	Weak transcription	Esophagus	oesophagus

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