Variant report

Variant	rs4804046
Chromosome Location	chr19:38839732-38839733
allele	G/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	CEBPB	chr19:38839495-38839853	A549	lung:	n/a	n/a
2	POLR2A	chr19:38839412-38839774	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38834987..38838242-chr19:38838656..38842905,5	MCF-7	breast:
2	chr19:38838273..38840146-chr19:38846615..38848893,2	MCF-7	breast:
3	chr19:38839437..38845026-chr19:38862738..38867726,6	MCF-7	breast:
4	chr19:38836592..38840441-chr19:38840696..38845039,4	K562	blood:

Variant related genes	Relation type
CATSPERG	TF binding region
ENSG00000099341	Chromatin interaction
ENSG00000099338	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11668355	0.85[EUR][1000 genomes]
rs11668651	0.89[AMR][1000 genomes]
rs11669131	0.83[AMR][1000 genomes]
rs11671779	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11672531	1.00[MEX][hapmap]
rs11672793	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11673012	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11673203	0.83[AMR][1000 genomes]
rs11673222	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12459746	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs2270093	0.96[EUR][1000 genomes]
rs2270094	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2270095	0.84[CEU][hapmap]
rs2286473	0.86[AMR][1000 genomes]
rs2286475	0.84[CEU][hapmap]
rs2286476	0.84[CEU][hapmap]
rs2302182	0.83[AMR][1000 genomes]
rs2302183	0.87[AMR][1000 genomes]
rs2304176	0.84[CEU][hapmap]
rs2304177	1.00[MEX][hapmap]
rs2368484	0.83[AMR][1000 genomes]
rs2887262	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3745951	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3745952	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3816044	1.00[MEX][hapmap]
rs4386247	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs45437199	0.95[EUR][1000 genomes]
rs4802327	1.00[MEX][hapmap]
rs4802351	1.00[ASW][hapmap];0.82[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs60082376	0.93[AMR][1000 genomes]
rs61091932	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7256575	0.86[AMR][1000 genomes]
rs73041302	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8101488	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8104823	0.88[MEX][hapmap]
rs8106900	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8112211	0.84[CEU][hapmap]
rs870218	0.88[MEX][hapmap]
rs931749	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs931750	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4804046	CYP2S1	cis	cerebellum	SCAN
rs4804046	SYCN	cis	parietal	SCAN
rs4804046	APOC4	cis	cerebellum	SCAN
rs4804046	SELV	cis	parietal	SCAN
rs4804046	LOC390940	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38828200-38840400	Weak transcription	Left Ventricle	heart
2	chr19:38828200-38841400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:38828200-38842000	Weak transcription	Brain Angular Gyrus	brain
4	chr19:38828200-38842600	Weak transcription	Esophagus	oesophagus
5	chr19:38828200-38844800	Weak transcription	Brain Substantia Nigra	brain
6	chr19:38828200-38852000	Weak transcription	Right Atrium	heart
7	chr19:38828400-38839800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr19:38828400-38839800	Weak transcription	Right Ventricle	heart
9	chr19:38828400-38840000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr19:38829400-38839800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr19:38830200-38844800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:38832200-38840400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr19:38833800-38840400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:38834200-38845000	Weak transcription	Spleen	Spleen
15	chr19:38835000-38842600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:38835200-38840200	Weak transcription	Brain Hippocampus Middle	brain
17	chr19:38835200-38840200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr19:38835200-38842600	Weak transcription	Fetal Muscle Leg	muscle
19	chr19:38835200-38847000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr19:38835200-38852000	Weak transcription	Pancreas	Pancrea
21	chr19:38836800-38845000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr19:38837200-38840200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr19:38837400-38842600	Weak transcription	Brain Germinal Matrix	brain
24	chr19:38837400-38842600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr19:38837800-38843000	Weak transcription	Fetal Intestine Small	intestine
26	chr19:38837800-38843800	Weak transcription	Fetal Brain Female	brain
27	chr19:38838200-38841800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr19:38838200-38843200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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