Variant report

Variant	rs1468773
Chromosome Location	chr19:57106401-57106402
allele	A/C/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	TCF12	chr19:57106192-57107068	A549	lung:	n/a	n/a
2	POLR2A	chr19:57106320-57106988	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr19:57106334-57106991	A549	lung:	n/a	n/a
4	SIN3A	chr19:57106292-57107129	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr19:57106303-57106977	GM12892	blood:	n/a	n/a
6	YY1	chr19:57106330-57106832	SK-N-SH_RA	brain:	n/a	chr19:57106621-57106635 chr19:57106757-57106771
7	MAX	chr19:57106283-57107149	A549	lung:	n/a	n/a
8	POLR2A	chr19:57106365-57106876	HepG2	liver:	n/a	n/a
9	CREB1	chr19:57106394-57106901	GM12878	blood:	n/a	n/a
10	YY1	chr19:57106279-57106929	A549	lung:	n/a	chr19:57106621-57106635 chr19:57106757-57106771
11	POLR2A	chr19:57106257-57106882	PFSK-1	brain:	n/a	n/a
12	TAF1	chr19:57106384-57106990	H1-hESC	embryonic stem cell:	n/a	n/a
13	FOXP2	chr19:57106361-57107043	PFSK-1	brain:	n/a	n/a
14	ZNF143	chr19:57106081-57106977	H1-hESC	embryonic stem cell:	n/a	chr19:57106768-57106786 chr19:57106597-57106615 chr19:57106835-57106845
15	YY1	chr19:57106364-57106862	GM12878	blood:	n/a	chr19:57106621-57106635 chr19:57106757-57106771
16	POLR2A	chr19:57106401-57107007	ECC-1	luminal epithelium:	n/a	n/a
17	BRCA1	chr19:57106394-57107029	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr19:57106334-57106974	H1-hESC	embryonic stem cell:	n/a	n/a
19	PAX5	chr19:57106333-57106678	GM12891	blood:	n/a	n/a
20	SP1	chr19:57106306-57106844	A549	lung:	n/a	n/a
21	TAF1	chr19:57106331-57107156	H1-neurons	neurons:	n/a	n/a
22	POLR2A	chr19:57106309-57107014	Gliobla	brain:	n/a	n/a
23	MXI1	chr19:57106379-57107236	IMR90	lung:	n/a	n/a
24	POLR2A	chr19:57106369-57106810	U87	brain:	n/a	n/a
25	PAX5	chr19:57106398-57106682	GM12878	blood:	n/a	n/a
26	MAZ	chr19:57106265-57107218	IMR90	lung:	n/a	n/a
27	POLR2A	chr19:57106217-57107256	H1-neurons	neurons:	n/a	n/a
28	TAF1	chr19:57106363-57107040	A549	lung:	n/a	n/a
29	POLR2A	chr19:57106390-57107091	HL-60	blood:	n/a	n/a
30	POLR2A	chr19:57106380-57106903	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:57106329-57106904	GM19099	blood:	n/a	n/a
32	REST	chr19:57106096-57107417	H1-neurons	neurons:	n/a	chr19:57106752-57106765 chr19:57106675-57106688 chr19:57107388-57107408
33	HNF4G	chr19:57106371-57106735	HepG2	liver:	n/a	n/a
34	ETS1	chr19:57106273-57106928	A549	lung:	n/a	chr19:57106576-57106587 chr19:57106801-57106814 chr19:57106604-57106617
35	POLR2A	chr19:57106233-57107423	H1-neurons	neurons:	n/a	n/a
36	RAD21	chr19:57106348-57106705	H1-hESC	embryonic stem cell:	n/a	n/a
37	ETS1	chr19:57106342-57106767	A549	lung:	n/a	chr19:57106576-57106587 chr19:57106604-57106617
38	POLR2A	chr19:57106331-57106920	GM15510	blood:	n/a	n/a
39	POLR2A	chr19:57106294-57107520	HepG2	liver:	n/a	n/a
40	CREB1	chr19:57106322-57106970	A549	lung:	n/a	n/a
41	MAX	chr19:57106198-57107345	A549	lung:	n/a	n/a
42	POLR2A	chr19:57106318-57107010	HUVEC	blood vessel:	n/a	n/a
43	YY1	chr19:57106328-57106860	SK-N-SH_RA	brain:	n/a	chr19:57106621-57106635 chr19:57106757-57106771
44	CHD2	chr19:57106401-57106800	GM12878	blood:	n/a	chr19:57106577-57106587
45	RCOR1	chr19:57106302-57106841	HepG2	liver:	n/a	n/a
46	MAZ	chr19:57106120-57106855	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr19:57106323-57106891	GM12878	blood:	n/a	n/a
48	POLR2A	chr19:57106334-57106826	Hela-S3	cervix:	n/a	n/a
49	YY1	chr19:57106352-57107031	GM12892	blood:	n/a	chr19:57106621-57106635 chr19:57106757-57106771
50	HCFC1	chr19:57106210-57107278	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
SIGLEC31P	TF binding region
ZNF71	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11667653	1.00[ASN][1000 genomes]
rs16987303	1.00[ASN][1000 genomes]
rs73059451	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv912518	chr19:56995737-57109821	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1062806	chr19:57050734-57191914	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1468773	ZNF460	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:57103000-57106800	Weak transcription	Fetal Heart	heart
2	chr19:57105800-57107000	Active TSS	Duodenum Mucosa	Duodenum
3	chr19:57105800-57107000	Active TSS	Fetal Kidney	kidney
4	chr19:57105800-57107000	Active TSS	Rectal Smooth Muscle	rectum
5	chr19:57105800-57107200	Active TSS	H1 Cell Line	embryonic stem cell
6	chr19:57105800-57107200	Active TSS	H9 Cell Line	embryonic stem cell
7	chr19:57105800-57107200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr19:57105800-57107200	Active TSS	Brain Anterior Caudate	brain
9	chr19:57105800-57107200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:57105800-57107200	Active TSS	Colon Smooth Muscle	Colon
11	chr19:57105800-57107400	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr19:57105800-57107800	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr19:57105800-57108200	ZNF genes & repeats	Liver	Liver
14	chr19:57106000-57106600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:57106000-57106600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr19:57106000-57106600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr19:57106000-57106600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:57106000-57106600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr19:57106000-57106800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:57106000-57106800	Active TSS	Brain Germinal Matrix	brain
21	chr19:57106000-57106800	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr19:57106000-57106800	Active TSS	Fetal Brain Female	brain
23	chr19:57106000-57106800	Active TSS	Stomach Smooth Muscle	stomach
24	chr19:57106000-57107000	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr19:57106000-57107000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr19:57106000-57107000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:57106000-57107000	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr19:57106000-57107200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:57106000-57107200	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr19:57106000-57107200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr19:57106000-57107200	Active TSS	Brain Hippocampus Middle	brain
32	chr19:57106000-57107200	Active TSS	Brain Substantia Nigra	brain
33	chr19:57106000-57107200	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr19:57106000-57107400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr19:57106000-57107400	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr19:57106000-57107400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:57106000-57107400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:57106000-57107400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr19:57106000-57107400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr19:57106000-57107800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:57106000-57107800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:57106000-57107800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr19:57106000-57107800	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr19:57106000-57107800	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr19:57106000-57107800	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr19:57106200-57106600	Active TSS	Right Atrium	heart
47	chr19:57106200-57106800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr19:57106200-57106800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr19:57106200-57106800	Active TSS	HMEC	breast
50	chr19:57106200-57107000	Active TSS	Primary T cells from cord blood	blood

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