Variant report

Variant	rs4805125
Chromosome Location	chr19:35896467-35896468
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	JUN	chr19:35896100-35896632	K562	blood:	n/a	chr19:35896253-35896261 chr19:35896251-35896263 chr19:35896229-35896238
2	YY1	chr19:35896017-35896570	GM12878	blood:	n/a	chr19:35896240-35896256 chr19:35896228-35896237
3	MAX	chr19:35895997-35896689	GM12878	blood:	n/a	n/a
4	TEAD4	chr19:35896093-35896635	K562	blood:	n/a	chr19:35896551-35896560
5	PAX5	chr19:35896089-35896482	GM12878	blood:	n/a	n/a
6	IRF4	chr19:35895900-35896669	GM12878	blood:	n/a	n/a
7	MAFK	chr19:35896341-35896468	HepG2	liver:	n/a	n/a
8	MTA3	chr19:35895817-35896609	GM12878	blood:	n/a	n/a
9	BHLHE40	chr19:35896200-35896490	HepG2	liver:	n/a	n/a
10	RUNX3	chr19:35895948-35896707	GM12878	blood:	n/a	n/a
11	IKZF1	chr19:35896000-35896711	GM12878	blood:	n/a	n/a
12	BHLHE40	chr19:35896093-35896527	K562	blood:	n/a	n/a
13	STAT3	chr19:35895956-35896585	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:35896451-35896529	MCF10A-Er-Src	breast:	n/a	n/a
15	MAZ	chr19:35896049-35896531	GM12878	blood:	n/a	n/a
16	EBF1	chr19:35896140-35896530	GM12878	blood:	n/a	n/a
17	CREB1	chr19:35895985-35896768	GM12878	blood:	n/a	n/a
18	EBF1	chr19:35896070-35896612	GM12878	blood:	n/a	n/a
19	MYC	chr19:35896046-35896674	MCF10A-Er-Src	breast:	n/a	n/a
20	RELA	chr19:35896109-35896563	GM12891	blood:	n/a	n/a
21	POLR2A	chr19:35895985-35896555	GM12892	blood:	n/a	n/a
22	MEF2A	chr19:35896030-35896553	GM12878	blood:	n/a	n/a
23	FOS	chr19:35896070-35896674	MCF10A-Er-Src	breast:	n/a	chr19:35896253-35896261 chr19:35896251-35896263 chr19:35896229-35896238
24	SIN3A	chr19:35896357-35896559	H1-hESC	embryonic stem cell:	n/a	n/a
25	FOS	chr19:35896050-35896659	MCF10A-Er-Src	breast:	n/a	chr19:35896253-35896261 chr19:35896251-35896263 chr19:35896229-35896238
26	YY1	chr19:35896070-35896642	GM12878	blood:	n/a	chr19:35896240-35896256 chr19:35896228-35896237
27	EP300	chr19:35896089-35896581	GM12878	blood:	n/a	chr19:35896503-35896510
28	NFATC1	chr19:35896042-35896571	GM12878	blood:	n/a	n/a
29	POLR2A	chr19:35895943-35896489	GM12878	blood:	n/a	n/a
30	TCF3	chr19:35896079-35896583	GM12878	blood:	n/a	n/a
31	FOS	chr19:35896065-35896595	MCF10A-Er-Src	breast:	n/a	chr19:35896253-35896261 chr19:35896251-35896263 chr19:35896229-35896238
32	EP300	chr19:35896076-35896565	GM12878	blood:	n/a	chr19:35896503-35896510
33	BATF	chr19:35895947-35896669	GM12878	blood:	n/a	chr19:35896254-35896264 chr19:35896458-35896467
34	ATF2	chr19:35895890-35896658	GM12878	blood:	n/a	n/a
35	POU2F2	chr19:35896090-35896619	GM12891	blood:	n/a	n/a
36	FOSL2	chr19:35895996-35896545	SK-N-SH	brain:	n/a	chr19:35896253-35896261 chr19:35896251-35896263 chr19:35896229-35896238
37	STAT3	chr19:35896044-35896657	MCF10A-Er-Src	breast:	n/a	n/a
38	BCLAF1	chr19:35896011-35896657	GM12878	blood:	n/a	chr19:35896227-35896236
39	FOXM1	chr19:35895915-35896784	GM12878	blood:	n/a	n/a
40	POU2F2	chr19:35896149-35896559	GM12878	blood:	n/a	n/a
41	STAT5A	chr19:35895851-35896570	GM12878	blood:	n/a	n/a
42	RELA	chr19:35896104-35896539	GM19193	blood:	n/a	n/a
43	PAX5	chr19:35896140-35896487	GM12878	blood:	n/a	n/a
44	TCF12	chr19:35896113-35896485	GM12878	blood:	n/a	n/a
45	TCF12	chr19:35896047-35896508	GM12878	blood:	n/a	n/a
46	CEBPB	chr19:35896156-35896571	Hela-S3	cervix:	n/a	n/a
47	BATF	chr19:35896157-35896595	GM12878	blood:	n/a	chr19:35896254-35896264 chr19:35896458-35896467
48	E2F4	chr19:35896175-35896528	MCF10A-Er-Src	breast:	n/a	chr19:35896228-35896237 chr19:35896473-35896480
49	CEBPB	chr19:35895988-35896734	GM12878	blood:	n/a	n/a
50	RAD21	chr19:35896096-35896529	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000205786	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11883057	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs12971509	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2097682	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2872084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35777556	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs386005	0.86[AMR][1000 genomes]
rs4806150	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4806151	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4806154	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7252182	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv833810	chr19:35782588-35971959	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
5	nsv2471	chr19:35837405-35903115	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv833811	chr19:35850257-36029535	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv911626	chr19:35856925-35896467	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv911627	chr19:35856925-35921266	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4805125	ZNF571	cis	parietal	SCAN
rs4805125	RASGRP4	cis	cerebellum	SCAN
rs4805125	FAM98C	cis	parietal	SCAN
rs4805125	CLC	cis	parietal	SCAN
rs4805125	ZNF569	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35886800-35899200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:35894600-35896800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:35894600-35900200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:35894800-35901000	Weak transcription	Right Ventricle	heart
5	chr19:35895200-35897400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr19:35895600-35897000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr19:35895800-35896600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr19:35895800-35896600	Enhancers	Placenta Amnion	Placenta Amnion
9	chr19:35895800-35896800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:35895800-35896800	Enhancers	HMEC	breast
11	chr19:35895800-35896800	Enhancers	NHEK	skin
12	chr19:35895800-35897000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr19:35895800-35897000	Enhancers	NHDF-Ad	bronchial
14	chr19:35895800-35897000	Enhancers	Osteobl	bone
15	chr19:35896000-35896600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:35896000-35896600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:35896000-35896800	Enhancers	Placenta	Placenta
18	chr19:35896000-35897000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:35896200-35896600	Enhancers	A549	lung
20	chr19:35896200-35896800	Enhancers	K562	blood
21	chr19:35896200-35898000	Enhancers	GM12878-XiMat	blood
22	chr19:35896400-35896600	Enhancers	Adipose Nuclei	Adipose
23	chr19:35896400-35896600	Enhancers	HepG2	liver
24	chr19:35896400-35897000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:35896400-35899200	Weak transcription	Spleen	Spleen

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