Variant report

Variant	rs98270
Chromosome Location	chr4:48019323-48019324
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	EGR1	chr4:48019219-48019518	GM12878	blood:	n/a	chr4:48019401-48019415 chr4:48019431-48019442 chr4:48019430-48019443 chr4:48019431-48019440
2	POLR2A	chr4:48018414-48019331	GM18505	blood:	n/a	n/a
3	E2F6	chr4:48018272-48019360	H1-hESC	embryonic stem cell:	n/a	chr4:48018748-48018762 chr4:48018778-48018787 chr4:48018739-48018748
4	MYC	chr4:48019097-48019373	MCF-7	breast:	n/a	chr4:48019176-48019183
5	MYC	chr4:48018503-48019580	MCF10A-Er-Src	breast:	n/a	chr4:48019432-48019441 chr4:48019176-48019183
6	TCF12	chr4:48018136-48019597	ECC-1	luminal epithelium:	n/a	chr4:48018588-48018598
7	FOS	chr4:48019088-48019449	HUVEC	blood vessel:	n/a	chr4:48019256-48019267 chr4:48019253-48019264 chr4:48019253-48019264
8	TFAP2C	chr4:48018288-48019589	Hela-S3	cervix:	n/a	n/a
9	CTBP2	chr4:48018238-48019635	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr4:48018853-48019333	H1-neurons	neurons:	n/a	n/a
11	CEBPB	chr4:48019219-48019560	IMR90	lung:	n/a	n/a
12	MAX	chr4:48018280-48019499	MCF-7	breast:	n/a	chr4:48019432-48019441 chr4:48019176-48019183
13	POLR2A	chr4:48019322-48019397	Gliobla	brain:	n/a	n/a
14	POLR2A	chr4:48019026-48019395	Hela-S3	cervix:	n/a	n/a
15	ZBTB33	chr4:48019089-48019567	HCT-116	colon:	n/a	n/a
16	CTCF	chr4:48017913-48019455	SK-N-SH	brain:	n/a	n/a
17	SIN3AK20	chr4:48019318-48019563	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr4:48018327-48019709	ECC-1	luminal epithelium:	n/a	n/a
19	MAX	chr4:48018361-48019401	H1-hESC	embryonic stem cell:	n/a	chr4:48019176-48019183
20	E2F4	chr4:48019228-48019455	MCF10A-Er-Src	breast:	n/a	n/a
21	MAX	chr4:48018329-48019563	ECC-1	luminal epithelium:	n/a	chr4:48019432-48019441 chr4:48019176-48019183
22	TBP	chr4:48018240-48019595	H1-hESC	embryonic stem cell:	n/a	n/a
23	REST	chr4:48018146-48019722	H1-neurons	neurons:	n/a	chr4:48018731-48018744 chr4:48018257-48018266 chr4:48018524-48018531
24	POLR2A	chr4:48018375-48019611	MCF-7	breast:	n/a	n/a
25	POLR2A	chr4:48018289-48019599	HCT-116	colon:	n/a	n/a
26	FOS	chr4:48019152-48019661	MCF10A-Er-Src	breast:	n/a	chr4:48019256-48019267 chr4:48019253-48019264 chr4:48019253-48019264
27	ELF1	chr4:48018147-48019831	GM12878	blood:	n/a	n/a
28	MAX	chr4:48018296-48019570	ECC-1	luminal epithelium:	n/a	chr4:48019432-48019441 chr4:48019176-48019183
29	HDAC2	chr4:48018262-48019503	MCF-7	breast:	n/a	n/a
30	CHD2	chr4:48019260-48019493	HepG2	liver:	n/a	n/a
31	EGR1	chr4:48019088-48019611	ECC-1	luminal epithelium:	n/a	chr4:48019401-48019415 chr4:48019431-48019442 chr4:48019430-48019443 chr4:48019431-48019440
32	FOS	chr4:48019143-48019630	MCF10A-Er-Src	breast:	n/a	chr4:48019256-48019267 chr4:48019253-48019264 chr4:48019253-48019264
33	POLR2A	chr4:48019297-48019392	HUVEC	blood vessel:	n/a	n/a
34	MYC	chr4:48019016-48019415	MCF10A-Er-Src	breast:	n/a	chr4:48019176-48019183
35	EBF1	chr4:48019163-48019471	GM12878	blood:	n/a	n/a
36	MAX	chr4:48018259-48019421	SK-N-SH	brain:	n/a	chr4:48019176-48019183
37	JUND	chr4:48018655-48019431	H1-hESC	embryonic stem cell:	n/a	chr4:48018779-48018788 chr4:48019256-48019267 chr4:48019253-48019264
38	EGR1	chr4:48019222-48019541	K562	blood:	n/a	chr4:48019401-48019415 chr4:48019431-48019442 chr4:48019430-48019443 chr4:48019431-48019440
39	STAT3	chr4:48018328-48019526	MCF10A-Er-Src	breast:	n/a	chr4:48018481-48018501
40	EP300	chr4:48018288-48019410	ECC-1	luminal epithelium:	n/a	chr4:48018731-48018747
41	EGR1	chr4:48019171-48019591	K562	blood:	n/a	chr4:48019401-48019415 chr4:48019431-48019442 chr4:48019430-48019443 chr4:48019431-48019440
42	MTA3	chr4:48018250-48019476	GM12878	blood:	n/a	n/a
43	ZBTB7A	chr4:48018405-48019660	ECC-1	luminal epithelium:	n/a	chr4:48018646-48018654 chr4:48019322-48019330
44	EGR1	chr4:48018269-48019729	HCT-116	colon:	n/a	chr4:48018958-48018965 chr4:48019401-48019415 chr4:48019431-48019442 chr4:48019430-48019443 chr4:48018778-48018788 chr4:48018734-48018747 chr4:48019431-48019440
45	HMGN3	chr4:48019300-48019448	K562	blood:	n/a	n/a
46	ZBTB7A	chr4:48018392-48019542	ECC-1	luminal epithelium:	n/a	chr4:48018646-48018654 chr4:48019322-48019330
47	E2F6	chr4:48018341-48019387	K562	blood:	n/a	chr4:48018748-48018762 chr4:48018778-48018787 chr4:48018739-48018748
48	POLR2A	chr4:48018149-48019426	H1-hESC	embryonic stem cell:	n/a	n/a
49	MAX	chr4:48018267-48019414	K562	blood:	n/a	chr4:48019176-48019183
50	MXI1	chr4:48018438-48019349	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48019190..48021605-chr4:48023120..48025588,2	K562	blood:
2	chr4:47914296..47917191-chr4:48017364..48021197,5	MCF-7	breast:

Variant related genes	Relation type
CNGA1	TF binding region
ENSG00000163293	Chromatin interaction
ENSG00000170448	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11722463	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11733284	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11736427	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13120847	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13125949	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13140968	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13142905	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13146880	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs224799	0.85[AFR][1000 genomes]
rs321622	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs321628	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs321630	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs321631	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs321632	0.82[AFR][1000 genomes]
rs321634	0.95[AFR][1000 genomes]
rs321635	0.82[AFR][1000 genomes]
rs4694879	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4695325	0.82[AFR][1000 genomes]
rs4695328	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6811245	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6832503	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6835057	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1013163	chr4:47977844-48022511	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv537084	chr4:47977844-48022511	Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs98270	NIPAL1	cis	lung	GTEx
rs98270	CNGA1	cis	Heart Left Ventricle	GTEx
rs98270	CNGA1	cis	Esophagus Muscularis	GTEx
rs98270	CNGA1	cis	Muscle Skeletal	GTEx
rs98270	CNGA1	cis	Adipose Subcutaneous	GTEx
rs98270	CNGA1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48017400-48020200	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr4:48017600-48020600	Active TSS	Rectal Smooth Muscle	rectum
3	chr4:48017800-48019600	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr4:48017800-48019800	Active TSS	Esophagus	oesophagus
5	chr4:48017800-48019800	Active TSS	Fetal Kidney	kidney
6	chr4:48018000-48019400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr4:48018000-48019400	Active TSS	Fetal Heart	heart
8	chr4:48018000-48019400	Active TSS	A549	lung
9	chr4:48018000-48019600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:48018000-48019600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:48018000-48019600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:48018000-48019600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr4:48018000-48019600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
14	chr4:48018000-48019600	Active TSS	Brain Substantia Nigra	brain
15	chr4:48018000-48019600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
16	chr4:48018000-48019600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
17	chr4:48018000-48019800	Active TSS	H9 Cell Line	embryonic stem cell
18	chr4:48018000-48019800	Active TSS	NH-A	brain
19	chr4:48018000-48020000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:48018000-48020400	Active TSS	Duodenum Mucosa	Duodenum
21	chr4:48018000-48020600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:48018200-48019400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr4:48018200-48019400	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr4:48018200-48019400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
25	chr4:48018200-48019600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr4:48018200-48019600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:48018200-48019600	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr4:48018200-48019600	Active TSS	Colon Smooth Muscle	Colon
29	chr4:48018200-48019600	Active TSS	Left Ventricle	heart
30	chr4:48018200-48019600	Active TSS	Pancreas	Pancrea
31	chr4:48018200-48019600	Active TSS	Right Ventricle	heart
32	chr4:48018200-48019800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:48018200-48019800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:48018200-48019800	Active TSS	Brain Anterior Caudate	brain
35	chr4:48018200-48019800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
36	chr4:48018200-48019800	Active TSS	Right Atrium	heart
37	chr4:48018200-48019800	Flanking Active TSS	HUVEC	blood vessel
38	chr4:48018200-48020000	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr4:48018400-48019400	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr4:48018400-48019400	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr4:48018400-48019400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:48018400-48019400	Active TSS	Ovary	ovary
43	chr4:48018400-48019600	Active TSS	Aorta	Aorta
44	chr4:48018400-48019600	Active TSS	Stomach Mucosa	stomach
45	chr4:48018400-48019600	Active TSS	Hela-S3	cervix
46	chr4:48018400-48019600	Active TSS	NHEK	skin
47	chr4:48018400-48019800	Active TSS	Gastric	stomach
48	chr4:48018400-48019800	Active TSS	Placenta Amnion	Placenta Amnion
49	chr4:48018400-48019800	Active TSS	Psoas Muscle	Psoas
50	chr4:48018400-48019800	Active TSS	Small Intestine	intestine

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