Variant report

Variant	rs57515712
Chromosome Location	chr4:7105199-7105200
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	POLR2A	chr4:7104663-7105276	K562	blood:	n/a	n/a
2	POLR2A	chr4:7104768-7105280	GM18505	blood:	n/a	n/a
3	POLR2A	chr4:7104890-7105893	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:7104807-7105294	Hela-S3	cervix:	n/a	n/a
5	MXI1	chr4:7104730-7105796	HepG2	liver:	n/a	n/a
6	IRF1	chr4:7104828-7105456	K562	blood:	n/a	chr4:7105135-7105149
7	POLR2A	chr4:7104877-7105383	NB4	blood:	n/a	n/a
8	MAZ	chr4:7104817-7105420	GM12878	blood:	n/a	chr4:7105138-7105148
9	MYC	chr4:7104814-7105204	K562	blood:	n/a	chr4:7105138-7105148
10	TAF1	chr4:7104917-7106010	HepG2	liver:	n/a	n/a
11	YY1	chr4:7104794-7105289	SK-N-SH_RA	brain:	n/a	n/a
12	POLR2A	chr4:7104832-7105254	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr4:7104573-7105390	K562	blood:	n/a	n/a
14	TAF1	chr4:7104865-7105274	A549	lung:	n/a	n/a
15	POLR2A	chr4:7104863-7105882	HepG2	liver:	n/a	n/a
16	YY1	chr4:7104752-7105291	K562	blood:	n/a	n/a
17	RCOR1	chr4:7104842-7105349	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr4:7104950-7105213	ProgFib	skin:	n/a	n/a
19	SP1	chr4:7104907-7105845	HepG2	liver:	n/a	chr4:7105138-7105148 chr4:7105590-7105602 chr4:7105138-7105147 chr4:7105137-7105149 chr4:7105139-7105148 chr4:7105591-7105600 chr4:7105138-7105148 chr4:7105115-7105129 chr4:7105137-7105149
20	HDAC2	chr4:7105170-7105790	HepG2	liver:	n/a	chr4:7105491-7105510
21	CHD2	chr4:7105020-7105542	HepG2	liver:	n/a	n/a
22	POLR2A	chr4:7104815-7105420	HCT-116	colon:	n/a	n/a
23	POLR2A	chr4:7104654-7105270	GM18951	blood:	n/a	n/a
24	TBP	chr4:7104766-7105284	K562	blood:	n/a	n/a
25	POLR2A	chr4:7104855-7105219	HCT-116	colon:	n/a	n/a
26	POLR2A	chr4:7104824-7105254	GM12878	blood:	n/a	n/a
27	POLR2A	chr4:7104719-7105253	K562	blood:	n/a	n/a
28	POLR2A	chr4:7104839-7106126	HepG2	liver:	n/a	n/a
29	HNF4A	chr4:7105110-7105862	HepG2	liver:	n/a	chr4:7105550-7105565 chr4:7105550-7105564 chr4:7105548-7105566 chr4:7105551-7105563 chr4:7105551-7105564 chr4:7105549-7105564 chr4:7105550-7105565 chr4:7105551-7105563 chr4:7105550-7105563
30	POLR2A	chr4:7104928-7105858	HepG2	liver:	n/a	n/a
31	MAX	chr4:7105190-7105656	ECC-1	luminal epithelium:	n/a	n/a
32	ZNF263	chr4:7104709-7105967	HEK293-T-REx	kidney:	n/a	n/a
33	POLR2A	chr4:7104760-7105375	MCF-7	breast:	n/a	n/a
34	NFIC	chr4:7104815-7105779	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr4:7104727-7105283	GM15510	blood:	n/a	n/a
36	TBP	chr4:7104910-7105822	HepG2	liver:	n/a	n/a
37	POLR2A	chr4:7104811-7105344	MCF-7	breast:	n/a	n/a
38	POLR2A	chr4:7104834-7105220	SK-N-MC	brain:	n/a	n/a
39	POLR2A	chr4:7104906-7105239	K562	blood:	n/a	n/a
40	POLR2A	chr4:7104837-7105256	MCF10A-Er-Src	breast:	n/a	n/a
41	PML	chr4:7104843-7105207	MCF-7	breast:	n/a	n/a
42	HEY1	chr4:7104791-7105866	HepG2	liver:	n/a	n/a
43	STAT1	chr4:7104999-7105305	GM12878	blood:	n/a	n/a
44	POLR2A	chr4:7104600-7105247	Raji	blood:	n/a	n/a
45	RFX5	chr4:7104935-7105344	Hela-S3	cervix:	n/a	n/a
46	TAF1	chr4:7104898-7105268	SK-N-SH	brain:	n/a	n/a
47	MAZ	chr4:7104690-7105638	K562	blood:	n/a	chr4:7105138-7105148
48	POLR2A	chr4:7104901-7105450	A549	lung:	n/a	n/a
49	POLR2A	chr4:7104847-7105430	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr4:7104814-7105453	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:7103913..7106622-chr4:7111535..7115141,3	K562	blood:
2	chr4:7105147..7106911-chr4:7141540..7143652,2	K562	blood:
3	chr4:7043790..7046279-chr4:7102506..7105292,2	K562	blood:
4	chr4:6783899..6786313-chr4:7103315..7105730,2	K562	blood:
5	chr4:7103913..7105517-chr4:7112314..7115141,2	K562	blood:

Variant related genes	Relation type
ENSG00000245468	TF binding region
ENSG00000170871	Chromatin interaction
ENSG00000173011	Chromatin interaction
ENSG00000200867	Chromatin interaction
ENSG00000173013	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10440167	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10516183	0.83[EUR][1000 genomes]
rs11930240	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11935906	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11939020	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11939101	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12642809	0.84[EUR][1000 genomes]
rs12643437	0.81[EUR][1000 genomes]
rs35322113	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60841350	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73202188	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34033	chr4:6973270-7390621	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv2757919	chr4:6988148-7269901	Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv2759221	chr4:6988148-7269901	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv428436	chr4:6988148-7269901	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv469847	chr4:7003525-7168441	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv878531	chr4:7006541-7129556	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv878534	chr4:7084985-7121880	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer 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	11 gene(s)	inside rSNPs	diseases
8	nsv878535	chr4:7093834-7135912	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv461191	chr4:7102597-7129001	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv878536	chr4:7102597-7142868	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv878537	chr4:7102597-7153642	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv878538	chr4:7102597-7158467	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57515712	RP11-367J11.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7103200-7105400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr4:7103400-7105200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr4:7103600-7105400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr4:7103600-7105400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr4:7103600-7105400	Active TSS	Brain Germinal Matrix	brain
6	chr4:7103600-7105600	Active TSS	A549	lung
7	chr4:7103600-7105600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr4:7103600-7105800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr4:7103600-7105800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr4:7103600-7106200	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr4:7103800-7105400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr4:7103800-7105400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:7103800-7105600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr4:7103800-7105600	Active TSS	Fetal Kidney	kidney
15	chr4:7103800-7105800	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr4:7103800-7105800	Flanking Active TSS	Liver	Liver
17	chr4:7104000-7105200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr4:7104000-7105400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr4:7104000-7105600	Active TSS	Aorta	Aorta
20	chr4:7104200-7105200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
21	chr4:7104200-7105200	Active TSS	Thymus	Thymus
22	chr4:7104200-7105400	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:7104200-7105400	Active TSS	Brain Angular Gyrus	brain
24	chr4:7104200-7105400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:7104200-7105400	Active TSS	Psoas Muscle	Psoas
26	chr4:7104200-7105600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr4:7104200-7105600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:7104200-7105600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:7104200-7105800	Active TSS	Right Atrium	heart
30	chr4:7104400-7105200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:7104400-7105200	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr4:7104400-7105200	Active TSS	Fetal Intestine Small	intestine
33	chr4:7104400-7105200	Active TSS	Lung	lung
34	chr4:7104400-7105200	Active TSS	Ovary	ovary
35	chr4:7104400-7105200	Active TSS	Right Ventricle	heart
36	chr4:7104400-7105200	Active TSS	NHDF-Ad	bronchial
37	chr4:7104400-7105400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
38	chr4:7104400-7105400	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr4:7104400-7105400	Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr4:7104400-7105400	Active TSS	Brain Hippocampus Middle	brain
41	chr4:7104400-7105400	Active TSS	Brain Substantia Nigra	brain
42	chr4:7104400-7105400	Active TSS	Colonic Mucosa	Colon
43	chr4:7104400-7105400	Active TSS	Fetal Intestine Large	intestine
44	chr4:7104400-7105400	Active TSS	Left Ventricle	heart
45	chr4:7104400-7105400	Active TSS	HepG2	liver
46	chr4:7104400-7105600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr4:7104400-7105600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
48	chr4:7104400-7105600	Enhancers	Fetal Heart	heart
49	chr4:7104400-7105800	Enhancers	Fetal Brain Male	brain
50	chr4:7104400-7106200	Flanking Active TSS	Stomach Smooth Muscle	stomach

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