Variant report

Variant	rs28417358
Chromosome Location	chr19:41428105-41428106
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	SP1	chr19:41426158-41428226	A549	lung:	n/a	n/a
2	EP300	chr19:41426058-41428275	A549	lung:	n/a	chr19:41427952-41427966
3	SIN3AK20	chr19:41426324-41428111	A549	lung:	n/a	n/a
4	SIX5	chr19:41426003-41428376	A549	lung:	n/a	n/a
5	EP300	chr19:41426278-41428262	A549	lung:	n/a	chr19:41427952-41427966
6	MAX	chr19:41426167-41428156	A549	lung:	n/a	n/a
7	SP1	chr19:41426223-41428603	A549	lung:	n/a	n/a
8	GABPA	chr19:41426507-41428106	A549	lung:	n/a	n/a
9	GATA3	chr19:41426095-41428186	A549	lung:	n/a	n/a
10	CEBPB	chr19:41426226-41428113	A549	lung:	n/a	chr19:41427674-41427685 chr19:41427674-41427685
11	TCF12	chr19:41426009-41428703	A549	lung:	n/a	n/a
12	FOSL2	chr19:41426058-41428179	A549	lung:	n/a	chr19:41427100-41427111
13	REST	chr19:41426064-41428338	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41220910..41226186-chr19:41426409..41429163,5	MCF-7	breast:

Variant related genes	Relation type
CYP2B7P	TF binding region
ENSG00000086544	Chromatin interaction
ENSG00000123815	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12150973	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12151139	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2161245	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4001944	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4609955	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56129017	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57274441	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72480748	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73034462	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034465	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038469	0.87[EUR][1000 genomes]
rs8100418	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758500	chr19:41291627-41546068	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2758762	chr19:41291627-41546068	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1066637	chr19:41309211-41597896	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv3337314	chr19:41388910-41534583	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv437830	chr19:41408746-41515702	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv437831	chr19:41416072-41524087	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41426200-41429800	Enhancers	Stomach Mucosa	stomach
2	chr19:41426400-41429600	Enhancers	Ovary	ovary
3	chr19:41426400-41430200	Enhancers	Fetal Intestine Large	intestine
4	chr19:41426400-41430200	Enhancers	Fetal Intestine Small	intestine
5	chr19:41426600-41428200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr19:41426600-41429000	Enhancers	K562	blood
7	chr19:41426600-41429600	Enhancers	Liver	Liver
8	chr19:41427000-41429200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:41427200-41428400	Enhancers	Placenta	Placenta
10	chr19:41427400-41428200	Flanking Active TSS	A549	lung
11	chr19:41427400-41428400	Enhancers	Duodenum Mucosa	Duodenum
12	chr19:41427600-41428200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:41427600-41428200	Enhancers	Colonic Mucosa	Colon
14	chr19:41427600-41428200	Weak transcription	Gastric	stomach
15	chr19:41427600-41428200	Enhancers	Small Intestine	intestine
16	chr19:41427600-41429800	Weak transcription	Pancreas	Pancrea
17	chr19:41427800-41428200	Enhancers	Lung	lung
18	chr19:41427800-41428400	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr19:41428000-41428200	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr19:41428000-41428600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr19:41428000-41429000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr19:41428000-41430200	Weak transcription	Hela-S3	cervix
23	chr19:41428000-41430800	Enhancers	Rectal Mucosa Donor 31	rectum

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