Variant report

Variant	rs66522479
Chromosome Location	chr19:57018997-57018998
allele	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	NRF1	chr19:57018621-57020372	SK-N-SH	brain:	n/a	chr19:57019014-57019028 chr19:57019208-57019219 chr19:57019011-57019025 chr19:57019016-57019025 chr19:57019210-57019219 chr19:57019208-57019222 chr19:57019014-57019025
2	CHD2	chr19:57018785-57019737	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr19:57018791-57019561	IMR90	lung:	n/a	chr19:57019188-57019198 chr19:57019273-57019287
4	POLR2A	chr19:57018979-57019262	H1-hESC	embryonic stem cell:	n/a	n/a
5	FOXP2	chr19:57018808-57019558	PFSK-1	brain:	n/a	n/a
6	MAX	chr19:57018756-57019215	H1-hESC	embryonic stem cell:	n/a	chr19:57018895-57018904
7	BACH1	chr19:57018807-57019161	H1-hESC	embryonic stem cell:	n/a	n/a
8	MXI1	chr19:57018571-57020457	IMR90	lung:	n/a	chr19:57020209-57020218
9	E2F6	chr19:57018749-57019196	H1-hESC	embryonic stem cell:	n/a	chr19:57019015-57019024
10	E2F6	chr19:57018562-57019214	H1-hESC	embryonic stem cell:	n/a	chr19:57019015-57019024
11	MXI1	chr19:57018675-57019492	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr19:57018632-57019643	ECC-1	luminal epithelium:	n/a	chr19:57019280-57019290 chr19:57018895-57018904
13	RAD21	chr19:57018649-57019187	H1-hESC	embryonic stem cell:	n/a	n/a
14	SIN3A	chr19:57018519-57020072	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr19:57018977-57019681	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr19:57018640-57020092	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr19:57018956-57019811	SK-N-MC	brain:	n/a	n/a
18	BRCA1	chr19:57018909-57019098	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZNF143	chr19:57018890-57019745	H1-hESC	embryonic stem cell:	n/a	chr19:57019091-57019101 chr19:57019407-57019425 chr19:57019407-57019416 chr19:57019409-57019418
20	REST	chr19:57018371-57020050	H1-neurons	neurons:	n/a	chr19:57018882-57018889
21	POLR2A	chr19:57018972-57019696	SK-N-SH	brain:	n/a	n/a
22	MYC	chr19:57018904-57019397	H1-hESC	embryonic stem cell:	n/a	chr19:57019280-57019290
23	POLR2A	chr19:57018930-57019851	Gliobla	brain:	n/a	n/a
24	CEBPB	chr19:57018866-57019252	IMR90	lung:	n/a	n/a
25	SIN3AK20	chr19:57018666-57019142	H1-hESC	embryonic stem cell:	n/a	n/a
26	JUND	chr19:57018923-57019299	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr19:57018827-57019676	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr19:57018659-57019690	SK-N-SH	brain:	n/a	chr19:57019280-57019290 chr19:57018895-57018904
29	CREB1	chr19:57018823-57019608	H1-hESC	embryonic stem cell:	n/a	n/a
30	NRF1	chr19:57018813-57019415	H1-hESC	embryonic stem cell:	n/a	chr19:57019014-57019028 chr19:57019208-57019219 chr19:57019011-57019025 chr19:57019016-57019025 chr19:57019210-57019219 chr19:57019208-57019222 chr19:57019014-57019025
31	SETDB1	chr19:57018560-57019103	U2OS	brain:	n/a	chr19:57019015-57019024
32	MXI1	chr19:57018355-57020592	SK-N-SH	brain:	n/a	chr19:57020209-57020218
33	MAZ	chr19:57018669-57020086	IMR90	lung:	n/a	chr19:57019280-57019290 chr19:57018895-57018904
34	POLR2A	chr19:57018736-57019515	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAX	chr19:57018555-57019580	SK-N-SH	brain:	n/a	chr19:57019280-57019290 chr19:57018895-57018904
36	SP1	chr19:57018823-57019510	H1-hESC	embryonic stem cell:	n/a	chr19:57019450-57019462 chr19:57019171-57019182
37	CREB1	chr19:57018946-57019211	A549	lung:	n/a	n/a
38	SIN3AK20	chr19:57018761-57019180	SK-N-SH	brain:	n/a	n/a
39	MAX	chr19:57018569-57019503	ECC-1	luminal epithelium:	n/a	chr19:57019280-57019290 chr19:57018895-57018904
40	POLR2A	chr19:57018674-57020096	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
ZNF471	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11084452	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667052	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11671776	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12151151	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12151254	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12978999	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12981980	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12986047	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs15507	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16987295	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16987310	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2215151	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2286422	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2869891	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3088221	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34269477	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35347939	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35664312	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35908973	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36020383	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36062917	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3813141	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3813142	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3813143	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4267437	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61144294	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62123030	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62124070	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7245557	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7250075	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8110306	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs917407	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs960997	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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	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	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	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
11	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs66522479	AC007228.11	cis	Esophagus Muscularis	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:57007800-57019200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:57017200-57019000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr19:57018200-57019600	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr19:57018200-57019800	Active TSS	Brain Hippocampus Middle	brain
5	chr19:57018200-57019800	Active TSS	Fetal Lung	lung
6	chr19:57018200-57020200	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr19:57018400-57019000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
8	chr19:57018400-57019000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:57018400-57019000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:57018400-57019000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
11	chr19:57018400-57019000	Flanking Active TSS	NHEK	skin
12	chr19:57018400-57019000	Flanking Active TSS	Osteobl	bone
13	chr19:57018400-57019400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
14	chr19:57018400-57019600	Active TSS	H1 Cell Line	embryonic stem cell
15	chr19:57018400-57019800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr19:57018400-57019800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr19:57018400-57019800	Active TSS	Brain Angular Gyrus	brain
18	chr19:57018400-57019800	Active TSS	Brain Cingulate Gyrus	brain
19	chr19:57018400-57019800	Active TSS	Brain Substantia Nigra	brain
20	chr19:57018400-57019800	Active TSS	Colon Smooth Muscle	Colon
21	chr19:57018400-57019800	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr19:57018400-57019800	Active TSS	Right Atrium	heart
23	chr19:57018400-57019800	Active TSS	HSMMtube	muscle
24	chr19:57018400-57019800	Active TSS	NHLF	lung
25	chr19:57018400-57020000	Active TSS	Psoas Muscle	Psoas
26	chr19:57018400-57020400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:57018400-57020400	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr19:57018600-57019000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:57018600-57019000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
30	chr19:57018600-57019000	Flanking Active TSS	Primary B cells from peripheral blood	blood
31	chr19:57018600-57019000	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr19:57018600-57019000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr19:57018600-57019000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr19:57018600-57019000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr19:57018600-57019000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:57018600-57019000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr19:57018600-57019000	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr19:57018600-57019000	Flanking Active TSS	Liver	Liver
39	chr19:57018600-57019000	ZNF genes & repeats	Colonic Mucosa	Colon
40	chr19:57018600-57019000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
41	chr19:57018600-57019000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr19:57018600-57019000	Flanking Active TSS	Fetal Brain Female	brain
43	chr19:57018600-57019000	ZNF genes & repeats	Fetal Intestine Small	intestine
44	chr19:57018600-57019000	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr19:57018600-57019000	Flanking Active TSS	Pancreas	Pancrea
46	chr19:57018600-57019000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr19:57018600-57019000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr19:57018600-57019000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr19:57018600-57019000	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr19:57018600-57019000	ZNF genes & repeats	Thymus	Thymus

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