Variant report

Variant	rs2304118
Chromosome Location	chr19:39440966-39440967
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	MAX	chr19:39440241-39441106	H1-hESC	embryonic stem cell:	n/a	chr19:39440401-39440411 chr19:39440442-39440452
2	PAX5	chr19:39440663-39441005	GM12878	blood:	n/a	n/a
3	FOSL2	chr19:39440600-39441320	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:39440625-39441096	A549	lung:	n/a	n/a
5	POLR2A	chr19:39440596-39441104	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:39440172-39440994	H1-hESC	embryonic stem cell:	n/a	n/a
7	EGR1	chr19:39440258-39441055	H1-hESC	embryonic stem cell:	n/a	chr19:39440442-39440452 chr19:39440484-39440494 chr19:39440403-39440416 chr19:39440401-39440411 chr19:39440460-39440467 chr19:39440403-39440416 chr19:39440402-39440416 chr19:39440443-39440453 chr19:39440591-39440601 chr19:39440594-39440603 chr19:39440402-39440417 chr19:39440593-39440606
8	MAX	chr19:39440338-39441221	ECC-1	luminal epithelium:	n/a	chr19:39440401-39440411 chr19:39440442-39440452
9	HEY1	chr19:39440890-39441320	HepG2	liver:	n/a	n/a
10	GABPA	chr19:39440700-39441054	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr19:39436715-39441620	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr19:39440172-39441095	A549	lung:	n/a	n/a
13	MXI1	chr19:39440146-39441502	SK-N-SH	brain:	n/a	n/a
14	PAX5	chr19:39440600-39441053	GM12878	blood:	n/a	n/a
15	MAX	chr19:39440397-39441203	ECC-1	luminal epithelium:	n/a	chr19:39440401-39440411 chr19:39440442-39440452
16	MAX	chr19:39440424-39441172	H1-hESC	embryonic stem cell:	n/a	chr19:39440442-39440452
17	PAX5	chr19:39440691-39441046	GM12892	blood:	n/a	n/a
18	USF1	chr19:39440617-39441081	ECC-1	luminal epithelium:	n/a	n/a
19	EGR1	chr19:39440221-39441101	ECC-1	luminal epithelium:	n/a	chr19:39440442-39440452 chr19:39440484-39440494 chr19:39440403-39440416 chr19:39440401-39440411 chr19:39440460-39440467 chr19:39440403-39440416 chr19:39440402-39440416 chr19:39440443-39440453 chr19:39440591-39440601 chr19:39440594-39440603 chr19:39440402-39440417 chr19:39440593-39440606
20	USF1	chr19:39440542-39441066	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr19:39440578-39441264	HepG2	liver:	n/a	n/a
22	E2F6	chr19:39440387-39441198	H1-hESC	embryonic stem cell:	n/a	chr19:39440395-39440410 chr19:39440485-39440494 chr19:39440592-39440601
23	POLR2A	chr19:39439957-39441354	SK-N-MC	brain:	n/a	n/a
24	CREB1	chr19:39440163-39441061	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr19:39428415-39444124	PANC-1	pancreas:	n/a	n/a
26	POLR2A	chr19:39432173-39442255	HepG2	liver:	n/a	n/a
27	CCNT2	chr19:39440848-39440967	K562	blood:	n/a	n/a
28	TCF12	chr19:39440456-39441126	ECC-1	luminal epithelium:	n/a	n/a
29	E2F6	chr19:39440346-39441096	H1-hESC	embryonic stem cell:	n/a	chr19:39440395-39440410 chr19:39440485-39440494 chr19:39440592-39440601
30	BHLHE40	chr19:39440713-39440998	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:39440787-39441542	HepG2	liver:	n/a	n/a
32	PAX5	chr19:39440720-39440966	GM12891	blood:	n/a	n/a
33	USF2	chr19:39440627-39440979	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr19:39440689-39441033	K562	blood:	n/a	n/a
35	POLR2A	chr19:39440137-39441024	H1-hESC	embryonic stem cell:	n/a	n/a
36	EGR1	chr19:39440279-39440977	ECC-1	luminal epithelium:	n/a	chr19:39440442-39440452 chr19:39440484-39440494 chr19:39440403-39440416 chr19:39440401-39440411 chr19:39440460-39440467 chr19:39440403-39440416 chr19:39440402-39440416 chr19:39440443-39440453 chr19:39440591-39440601 chr19:39440594-39440603 chr19:39440402-39440417 chr19:39440593-39440606
37	POLR2A	chr19:39440504-39440977	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr19:39440603-39441541	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:39440924-39440974	HCM	heart:	n/a
2	chr19:39440924-39440974	GM12891	blood:	n/a
3	chr19:39440924-39440974	SKMC	muscle:	n/a
4	chr19:39440924-39440974	AG04449	skin:	fetal
5	chr19:39440924-39440974	RPTEC	kidney:	n/a
6	chr19:39440924-39440974	GM19239	blood:	n/a
7	chr19:39440924-39440974	NH-A	brain:	n/a
8	chr19:39440924-39440974	HRE	kidney:	n/a
9	chr19:39440924-39440974	U87	brain:	n/a
10	chr19:39440924-39440974	HNPCEpiC	eye:	n/a
11	chr19:39440924-39440974	HCPEpiC	choroid plexus:	n/a
12	chr19:39440924-39440974	SK-N-MC	brain:	n/a
13	chr19:39440924-39440974	HMEC	breast:	n/a
14	chr19:39440924-39440974	GM12892	blood:	n/a
15	chr19:39440924-39440974	HAEpiC	amniotic membrane:	n/a
16	chr19:39440924-39440974	AG04450	lung:	fetal
17	chr19:39440924-39440974	BJ	skin:	n/a
18	chr19:39440924-39440974	GM12878	blood:	n/a
19	chr19:39440924-39440974	HRCEpiC	kidney:	n/a
20	chr19:39440924-39440974	IMR90	lung:	fetal
21	chr19:39440924-39440974	BE2_C	brain:	n/a
22	chr19:39440924-39440974	GM06990	blood:	n/a
23	chr19:39440924-39440974	ECC-1	luminal epithelium:	n/a
24	chr19:39440924-39440974	MCF-7	breast:	n/a
25	chr19:39440924-39440974	T-47D	breast:	n/a
26	chr19:39440924-39440974	HPAEpiC	pulmonary alveolar:	n/a
27	chr19:39440924-39440974	HIPEpiC	eye:	n/a
28	chr19:39440924-39440974	AG09319	gingival:	n/a
29	chr19:39440924-39440974	SAEC	small airway:	n/a
30	chr19:39440924-39440974	LNCaP	prostate:	n/a
31	chr19:39440924-39440974	Jurkat	blood:	n/a
32	chr19:39440924-39440974	SK-N-SH_RA	brain:	n/a
33	chr19:39440924-39440974	HRPEpiC	eye:	n/a
34	chr19:39440924-39440974	ovcar-3	ovarian:	n/a
35	chr19:39440924-39440974	K562	blood:	n/a
36	chr19:39440924-39440974	HEEpiC	esophagus:	n/a
37	chr19:39440924-39440974	AG10803	skin:	n/a
38	chr19:39440924-39440974	NT2-D1	testis:	n/a
39	chr19:39440924-39440974	HCF	heart:	n/a
40	chr19:39440924-39440974	ProgFib	skin:	n/a
41	chr19:39440924-39440974	HL-60	blood:	n/a
42	chr19:39440924-39440974	H1-hESC	embryonic stem cell:	embryo
43	chr19:39440924-39440974	HCT-116	colon:	n/a
44	chr19:39440924-39440974	AG09309	skin:	n/a
45	chr19:39440924-39440974	NHDF-neo	bronchial:	n/a
46	chr19:39440924-39440974	Hepatocyte	liver:	n/a
47	chr19:39440924-39440974	A549	lung:	n/a
48	chr19:39440924-39440974	HepG2	liver:	n/a
49	chr19:39440924-39440974	CMK	blood:	n/a
50	chr19:39440924-39440974	HEK293	kidney:	embryo

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39421083..39425618-chr19:39435632..39441753,7	MCF-7	breast:
2	chr19:39420306..39422739-chr19:39440304..39443002,2	K562	blood:

Variant related genes	Relation type
SARS2	TF binding region
ENSG00000269547	TF binding region
FBXO17	TF binding region
SARS2	CpG island
ENSG00000269547	CpG island
FBXO17	CpG island
ENSG00000128626	Chromatin interaction
ENSG00000104835	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12460412	0.89[ASN][1000 genomes]
rs2304117	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39422600-39453000	Weak transcription	HSMMtube	muscle
2	chr19:39432400-39441800	Strong transcription	A549	lung
3	chr19:39435600-39442800	Weak transcription	Fetal Kidney	kidney
4	chr19:39435800-39453000	Weak transcription	K562	blood
5	chr19:39437200-39443000	Weak transcription	HSMM	muscle
6	chr19:39438200-39447000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:39438400-39453000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr19:39439200-39452600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:39439400-39442800	Weak transcription	HepG2	liver
10	chr19:39439600-39446200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:39440000-39441400	Active TSS	Fetal Brain Female	brain
12	chr19:39440200-39441000	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr19:39440200-39441000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:39440200-39441000	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr19:39440200-39441000	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr19:39440200-39441000	Active TSS	Brain Anterior Caudate	brain
17	chr19:39440200-39441000	Active TSS	Brain Substantia Nigra	brain
18	chr19:39440200-39441200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:39440200-39441200	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr19:39440200-39441200	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr19:39440200-39441200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
22	chr19:39440200-39441200	Enhancers	Primary hematopoietic stem cells	blood
23	chr19:39440200-39441200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr19:39440200-39441200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:39440200-39441200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:39440200-39441200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr19:39440200-39441200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr19:39440200-39441200	Active TSS	Brain Germinal Matrix	brain
29	chr19:39440200-39441200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr19:39440200-39441200	ZNF genes & repeats	Fetal Intestine Large	intestine
31	chr19:39440200-39441200	Enhancers	Placenta	Placenta
32	chr19:39440200-39441400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
33	chr19:39440200-39441400	Enhancers	Small Intestine	intestine
34	chr19:39440400-39441000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:39440400-39441000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr19:39440400-39441000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
37	chr19:39440400-39441200	Enhancers	Primary B cells from cord blood	blood
38	chr19:39440400-39441200	Enhancers	Spleen	Spleen
39	chr19:39440400-39441400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr19:39440600-39441000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr19:39440600-39441000	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:39440600-39441000	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr19:39440600-39441000	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr19:39440600-39441000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:39440600-39441000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:39440600-39441000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
47	chr19:39440600-39441000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
48	chr19:39440600-39441000	Enhancers	Aorta	Aorta
49	chr19:39440600-39441000	Active TSS	Colon Smooth Muscle	Colon
50	chr19:39440600-39441000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum

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