Variant report

Variant	rs12986299
Chromosome Location	chr19:40338206-40338207
allele	A/C
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	FOXA1	chr19:40338143-40338479	HepG2	liver:	n/a	n/a
2	CEBPB	chr19:40338017-40338406	HepG2	liver:	n/a	chr19:40338126-40338139 chr19:40338126-40338137 chr19:40338128-40338137
3	FOXA2	chr19:40338133-40338513	HepG2	liver:	n/a	n/a
4	FOXA1	chr19:40338131-40338507	T-47D	breast:	n/a	n/a
5	FOXA1	chr19:40338078-40338490	HepG2	liver:	n/a	n/a
6	FOXA1	chr19:40338108-40338439	HepG2	liver:	n/a	n/a
7	MYC	chr19:40334790-40338257	A549	lung:	n/a	chr19:40337007-40337014 chr19:40337006-40337015
8	POLR2A	chr19:40306432-40338982	PANC-1	pancreas:	n/a	n/a
9	SIN3AK20	chr19:40332892-40340524	PANC-1	pancreas:	n/a	n/a
10	CTCF	chr19:40334289-40338535	A549	lung:	n/a	chr19:40336774-40336782 chr19:40336634-40336647
11	GATA3	chr19:40338112-40338688	MCF-7	breast:	n/a	n/a
12	SIN3AK20	chr19:40334304-40340581	PANC-1	pancreas:	n/a	n/a
13	TEAD4	chr19:40338073-40338627	HepG2	liver:	n/a	n/a
14	CEBPB	chr19:40338022-40338258	K562	blood:	n/a	chr19:40338126-40338139 chr19:40338126-40338137 chr19:40338128-40338137
15	FOXA1	chr19:40338044-40338573	HepG2	liver:	n/a	n/a
16	CEBPB	chr19:40338002-40338294	IMR90	lung:	n/a	chr19:40338126-40338139 chr19:40338126-40338137 chr19:40338128-40338137

No.	Distal block	Cell Line	Cell type
1	chr19:40327985..40330266-chr19:40338198..40340868,2	MCF-7	breast:
2	chr19:40337132..40339013-chr19:40340235..40342919,2	MCF-7	breast:
3	chr19:40330455..40332873-chr19:40336316..40338752,3	MCF-7	breast:
4	chr19:40335423..40338376-chr19:40475745..40478585,3	MCF-7	breast:
5	chr19:40337506..40339114-chr19:40356435..40358897,2	MCF-7	breast:
6	chr19:40322842..40325581-chr19:40335629..40338491,6	MCF-7	breast:
7	chr19:40337126..40339206-chr19:40352976..40355937,2	K562	blood:
8	chr19:40294943..40296744-chr19:40337305..40340033,2	MCF-7	breast:
9	chr19:40321340..40326326-chr19:40333108..40338214,12	MCF-7	breast:
10	chr19:40338036..40340893-chr19:40348527..40351769,3	MCF-7	breast:

Variant related genes	Relation type
FBL	TF binding region
ENSG00000105204	Chromatin interaction
ENSG00000013275	Chromatin interaction
ENSG00000105202	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10422280	0.83[CHB][hapmap]
rs11880094	0.84[CHB][hapmap]
rs11880956	0.82[CHB][hapmap]
rs11883249	0.84[CHB][hapmap]
rs12975624	0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[TSI][hapmap]
rs12980289	0.84[CHB][hapmap]
rs2072290	0.84[CHB][hapmap]
rs3810383	0.84[CHB][hapmap]
rs4803297	0.84[CHB][hapmap]
rs4803298	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs616650	0.84[CHB][hapmap]
rs718066	0.84[CHB][hapmap]
rs7253739	0.84[CHB][hapmap]

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	esv3329492	chr19:40198535-40437035	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv911696	chr19:40310497-40344648	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv9725	chr19:40315519-40412523	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12986299	NPAS1	cis	cerebellum	SCAN
rs12986299	PHLDB3	cis	parietal	SCAN
rs12986299	ERF	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40336600-40338400	Active TSS	Stomach Mucosa	stomach
2	chr19:40337200-40338400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr19:40337400-40338400	Enhancers	Placenta Amnion	Placenta Amnion
4	chr19:40337400-40338600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr19:40337600-40338400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr19:40337600-40338400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:40337600-40338400	Enhancers	Fetal Heart	heart
8	chr19:40337600-40338400	Enhancers	Fetal Intestine Large	intestine
9	chr19:40337600-40338400	Enhancers	Fetal Lung	lung
10	chr19:40337600-40338400	Enhancers	Fetal Muscle Leg	muscle
11	chr19:40337600-40338400	Enhancers	Fetal Stomach	stomach
12	chr19:40337600-40338600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr19:40337600-40339400	Enhancers	Placenta	Placenta
14	chr19:40337800-40338400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:40337800-40338400	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr19:40337800-40338400	Enhancers	Fetal Intestine Small	intestine
17	chr19:40337800-40338400	Enhancers	Stomach Smooth Muscle	stomach
18	chr19:40337800-40338400	Enhancers	A549	lung
19	chr19:40337800-40338600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr19:40337800-40338600	Weak transcription	Right Atrium	heart
21	chr19:40337800-40338800	Weak transcription	Thymus	Thymus
22	chr19:40338000-40338400	Enhancers	Duodenum Mucosa	Duodenum
23	chr19:40338000-40338400	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr19:40338000-40339000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr19:40338000-40340000	Enhancers	HepG2	liver
26	chr19:40338000-40341400	Weak transcription	Hela-S3	cervix
27	chr19:40338200-40338400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:40338200-40338400	Enhancers	K562	blood

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