Variant report

Variant	rs12462715
Chromosome Location	chr19:40168701-40168702
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	FOXA2	chr19:40168601-40169214	HepG2	liver:	n/a	n/a
2	FOXA2	chr19:40168480-40169086	A549	lung:	n/a	n/a
3	MAFK	chr19:40168623-40168913	Hela-S3	cervix:	n/a	chr19:40168738-40168753
4	NFIC	chr19:40168553-40170977	GM12878	blood:	n/a	n/a
5	MAFK	chr19:40168580-40168938	HepG2	liver:	n/a	chr19:40168738-40168753
6	MAFF	chr19:40168586-40168942	HepG2	liver:	n/a	chr19:40168736-40168754
7	FOXA1	chr19:40168522-40169018	HepG2	liver:	n/a	chr19:40168778-40168793
8	STAT3	chr19:40168678-40169057	MCF10A-Er-Src	breast:	n/a	chr19:40168934-40168943 chr19:40168935-40168944 chr19:40168929-40168949 chr19:40168933-40168944 chr19:40168932-40168946 chr19:40168839-40168850
9	MAX	chr19:40168547-40169052	MCF-7	breast:	n/a	n/a
10	MAFK	chr19:40168583-40168936	HepG2	liver:	n/a	chr19:40168738-40168753
11	STAT3	chr19:40168692-40169129	MCF10A-Er-Src	breast:	n/a	chr19:40168934-40168943 chr19:40168935-40168944 chr19:40168929-40168949 chr19:40168933-40168944 chr19:40168932-40168946 chr19:40168839-40168850
12	FOXA1	chr19:40168612-40168903	ECC-1	luminal epithelium:	n/a	chr19:40168778-40168793
13	FOXA1	chr19:40168608-40169026	HepG2	liver:	n/a	chr19:40168778-40168793
14	FOXA2	chr19:40168483-40169006	A549	lung:	n/a	n/a
15	MTA3	chr19:40168531-40172519	GM12878	blood:	n/a	n/a
16	FOXA2	chr19:40168594-40168857	HepG2	liver:	n/a	n/a
17	FOXA1	chr19:40168632-40168883	ECC-1	luminal epithelium:	n/a	chr19:40168778-40168793
18	PRDM1	chr19:40168623-40169061	Hela-S3	cervix:	n/a	chr19:40168899-40168913 chr19:40168837-40168851 chr19:40168838-40168851 chr19:40168900-40168913 chr19:40168836-40168851
19	STAT1	chr19:40168657-40169174	Hela-S3	cervix:	n/a	chr19:40168934-40168943 chr19:40168935-40168944 chr19:40168929-40168949 chr19:40168932-40168946 chr19:40168839-40168850
20	FOXA1	chr19:40168614-40168929	HepG2	liver:	n/a	chr19:40168778-40168793
21	FOXA1	chr19:40168597-40168998	T-47D	breast:	n/a	chr19:40168778-40168793
22	FOXA1	chr19:40168548-40168896	HepG2	liver:	n/a	chr19:40168778-40168793
23	FOXA1	chr19:40168559-40168933	T-47D	breast:	n/a	chr19:40168778-40168793

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40166260..40168931-chr19:40253973..40255544,2	MCF-7	breast:
2	chr19:40166471..40169299-chr19:40170755..40172585,2	K562	blood:

Variant related genes	Relation type
ENSG00000226025	TF binding region
ENSG00000226025	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10414838	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10422118	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083532	0.81[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs11881797	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461429	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12463262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13344378	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55976926	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62119909	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057361	chr19:40123868-40310996	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv2482	chr19:40125797-40170766	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3413868	chr19:40130700-40184720	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1061361	chr19:40131820-40310996	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv579511	chr19:40132825-40310497	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1062394	chr19:40133229-40310186	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv544004	chr19:40133229-40310186	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv3355956	chr19:40135051-40188792	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	esv3998	chr19:40135120-40188646	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	esv3397881	chr19:40150495-40199437	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv963047	chr19:40151942-40168890	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40162600-40169600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:40164400-40168800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:40166200-40169600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr19:40166200-40169600	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr19:40167000-40168800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:40167400-40169600	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr19:40168000-40168800	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr19:40168000-40169800	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr19:40168200-40170000	Enhancers	Fetal Muscle Leg	muscle
10	chr19:40168200-40170400	Enhancers	Placenta	Placenta
11	chr19:40168400-40168800	Enhancers	Fetal Muscle Trunk	muscle
12	chr19:40168400-40170200	Enhancers	Psoas Muscle	Psoas
13	chr19:40168400-40170600	Enhancers	Left Ventricle	heart
14	chr19:40168400-40170600	Enhancers	HepG2	liver
15	chr19:40168400-40171200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr19:40168600-40168800	Enhancers	Esophagus	oesophagus
17	chr19:40168600-40168800	Bivalent/Poised TSS	A549	lung
18	chr19:40168600-40169200	Flanking Active TSS	Liver	Liver
19	chr19:40168600-40169200	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr19:40168600-40169400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr19:40168600-40169600	Enhancers	Duodenum Mucosa	Duodenum
22	chr19:40168600-40169800	Enhancers	Primary T cells fromperipheralblood	blood
23	chr19:40168600-40169800	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr19:40168600-40169800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr19:40168600-40170000	Enhancers	Gastric	stomach
26	chr19:40168600-40170400	Enhancers	Brain Anterior Caudate	brain
27	chr19:40168600-40170600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr19:40168600-40170600	Enhancers	Adipose Nuclei	Adipose
29	chr19:40168600-40170600	Enhancers	Lung	lung
30	chr19:40168600-40170600	Enhancers	Pancreas	Pancrea
31	chr19:40168600-40170600	Enhancers	Right Ventricle	heart
32	chr19:40168600-40170800	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr19:40168600-40171600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:40168600-40172600	Flanking Active TSS	GM12878-XiMat	blood

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