Variant report

Variant	rs321635
Chromosome Location	chr4:48019528-48019529
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	MYC	chr4:48018503-48019580	MCF10A-Er-Src	breast:	n/a	chr4:48019432-48019441 chr4:48019176-48019183
2	TCF12	chr4:48018136-48019597	ECC-1	luminal epithelium:	n/a	chr4:48018588-48018598
3	TFAP2C	chr4:48018288-48019589	Hela-S3	cervix:	n/a	n/a
4	CTBP2	chr4:48018238-48019635	H1-hESC	embryonic stem cell:	n/a	n/a
5	CEBPB	chr4:48019219-48019560	IMR90	lung:	n/a	n/a
6	ZBTB33	chr4:48019089-48019567	HCT-116	colon:	n/a	n/a
7	SIN3AK20	chr4:48019318-48019563	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr4:48018327-48019709	ECC-1	luminal epithelium:	n/a	n/a
9	JUN	chr4:48019479-48019560	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr4:48018329-48019563	ECC-1	luminal epithelium:	n/a	chr4:48019432-48019441 chr4:48019176-48019183
11	TBP	chr4:48018240-48019595	H1-hESC	embryonic stem cell:	n/a	n/a
12	REST	chr4:48018146-48019722	H1-neurons	neurons:	n/a	chr4:48018731-48018744 chr4:48018257-48018266 chr4:48018524-48018531
13	POLR2A	chr4:48018375-48019611	MCF-7	breast:	n/a	n/a
14	POLR2A	chr4:48018289-48019599	HCT-116	colon:	n/a	n/a
15	FOS	chr4:48019152-48019661	MCF10A-Er-Src	breast:	n/a	chr4:48019256-48019267 chr4:48019253-48019264 chr4:48019253-48019264
16	ELF1	chr4:48018147-48019831	GM12878	blood:	n/a	n/a
17	MAX	chr4:48018296-48019570	ECC-1	luminal epithelium:	n/a	chr4:48019432-48019441 chr4:48019176-48019183
18	EGR1	chr4:48019088-48019611	ECC-1	luminal epithelium:	n/a	chr4:48019401-48019415 chr4:48019431-48019442 chr4:48019430-48019443 chr4:48019431-48019440
19	FOS	chr4:48019143-48019630	MCF10A-Er-Src	breast:	n/a	chr4:48019256-48019267 chr4:48019253-48019264 chr4:48019253-48019264
20	EGR1	chr4:48019222-48019541	K562	blood:	n/a	chr4:48019401-48019415 chr4:48019431-48019442 chr4:48019430-48019443 chr4:48019431-48019440
21	EGR1	chr4:48019171-48019591	K562	blood:	n/a	chr4:48019401-48019415 chr4:48019431-48019442 chr4:48019430-48019443 chr4:48019431-48019440
22	ZBTB7A	chr4:48018405-48019660	ECC-1	luminal epithelium:	n/a	chr4:48018646-48018654 chr4:48019322-48019330
23	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
24	ZBTB7A	chr4:48018392-48019542	ECC-1	luminal epithelium:	n/a	chr4:48018646-48018654 chr4:48019322-48019330
25	POLR2A	chr4:48018385-48019620	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr4:48018351-48019731	MCF-7	breast:	n/a	n/a
27	POLR2A	chr4:48018403-48019615	IMR90	lung:	n/a	n/a
28	CHD2	chr4:48019212-48019544	H1-hESC	embryonic stem cell:	n/a	n/a
29	ZNF263	chr4:48018354-48019801	HEK293-T-REx	kidney:	n/a	n/a
30	HA-E2F1	chr4:48018178-48019571	MCF-7	breast:	n/a	chr4:48018748-48018762 chr4:48018778-48018787 chr4:48018739-48018748
31	POLR2A	chr4:48018496-48019731	MCF10A-Er-Src	breast:	n/a	n/a
32	EGR1	chr4:48019134-48019682	MCF-7	breast:	n/a	chr4:48019401-48019415 chr4:48019431-48019442 chr4:48019430-48019443 chr4:48019431-48019440
33	POLR2A	chr4:48018401-48019662	Hela-S3	cervix:	n/a	n/a
34	PML	chr4:48018104-48019724	GM12878	blood:	n/a	n/a
35	JUN	chr4:48018089-48019548	K562	blood:	n/a	chr4:48018779-48018788 chr4:48019256-48019267 chr4:48019253-48019264
36	FOS	chr4:48019137-48019595	MCF10A-Er-Src	breast:	n/a	chr4:48019256-48019267 chr4:48019253-48019264 chr4:48019253-48019264
37	EGR1	chr4:48019226-48019664	ECC-1	luminal epithelium:	n/a	chr4:48019401-48019415 chr4:48019431-48019442 chr4:48019430-48019443 chr4:48019431-48019440
38	POLR2A	chr4:48018525-48019528	MCF-7	breast:	n/a	n/a
39	SIN3AK20	chr4:48018235-48019585	MCF-7	breast:	n/a	n/a
40	POLR2A	chr4:48018421-48019773	MCF10A-Er-Src	breast:	n/a	n/a
41	SIN3A	chr4:48018046-48019563	H1-hESC	embryonic stem cell:	n/a	chr4:48018690-48018699
42	POLR2A	chr4:48018984-48019544	HCT-116	colon:	n/a	n/a
43	EGR1	chr4:48018325-48019793	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

No.	Distal block	Cell Line	Cell type
1	chr4:48019190..48021605-chr4:48023120..48025588,2	K562	blood:
2	chr4:48019513..48022096-chr4:48074921..48077158,2	MCF-7	breast:
3	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: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs13116684	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13121957	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13145218	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13150783	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13151608	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs224799	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs321628	0.81[AFR][1000 genomes]
rs321630	0.81[AFR][1000 genomes]
rs321631	0.81[AFR][1000 genomes]
rs321632	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs321634	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35085584	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4695325	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55670663	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6447609	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6812991	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7674929	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs98270	0.82[AFR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs321635	CNGA1	cis	Thyroid	GTEx

Chromatin state (count:120 , 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	chr4:48018000-48019600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:48018000-48019600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:48018000-48019600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:48018000-48019600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr4:48018000-48019600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
11	chr4:48018000-48019600	Active TSS	Brain Substantia Nigra	brain
12	chr4:48018000-48019600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
13	chr4:48018000-48019600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
14	chr4:48018000-48019800	Active TSS	H9 Cell Line	embryonic stem cell
15	chr4:48018000-48019800	Active TSS	NH-A	brain
16	chr4:48018000-48020000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:48018000-48020400	Active TSS	Duodenum Mucosa	Duodenum
18	chr4:48018000-48020600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:48018200-48019600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:48018200-48019600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:48018200-48019600	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr4:48018200-48019600	Active TSS	Colon Smooth Muscle	Colon
23	chr4:48018200-48019600	Active TSS	Left Ventricle	heart
24	chr4:48018200-48019600	Active TSS	Pancreas	Pancrea
25	chr4:48018200-48019600	Active TSS	Right Ventricle	heart
26	chr4:48018200-48019800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:48018200-48019800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr4:48018200-48019800	Active TSS	Brain Anterior Caudate	brain
29	chr4:48018200-48019800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
30	chr4:48018200-48019800	Active TSS	Right Atrium	heart
31	chr4:48018200-48019800	Flanking Active TSS	HUVEC	blood vessel
32	chr4:48018200-48020000	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr4:48018400-48019600	Active TSS	Aorta	Aorta
34	chr4:48018400-48019600	Active TSS	Stomach Mucosa	stomach
35	chr4:48018400-48019600	Active TSS	Hela-S3	cervix
36	chr4:48018400-48019600	Active TSS	NHEK	skin
37	chr4:48018400-48019800	Active TSS	Gastric	stomach
38	chr4:48018400-48019800	Active TSS	Placenta Amnion	Placenta Amnion
39	chr4:48018400-48019800	Active TSS	Psoas Muscle	Psoas
40	chr4:48018400-48019800	Active TSS	Small Intestine	intestine
41	chr4:48018400-48020400	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr4:48018600-48019600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr4:48018600-48019600	Bivalent/Poised TSS	HepG2	liver
44	chr4:48018600-48019800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:48018600-48019800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr4:48018600-48019800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
47	chr4:48018600-48020000	Bivalent/Poised TSS	Fetal Stomach	stomach
48	chr4:48018600-48020200	Active TSS	HMEC	breast
49	chr4:48018600-48020600	Active TSS	Colonic Mucosa	Colon
50	chr4:48018800-48019600	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--

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