Variant report

Variant	rs321634
Chromosome Location	chr4:48018614-48018615
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:209)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:209 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:48018318-48018969	HepG2	liver:	n/a	n/a
2	MYC	chr4:48018345-48018992	K562	blood:	n/a	n/a
3	CEBPB	chr4:48018547-48018683	A549	lung:	n/a	n/a
4	CTCF	chr4:48018520-48018670	A549	lung:	n/a	n/a
5	POLR2A	chr4:48018414-48019331	GM18505	blood:	n/a	n/a
6	NR2F2	chr4:48018230-48019080	MCF-7	breast:	n/a	n/a
7	MAZ	chr4:48018347-48019012	K562	blood:	n/a	n/a
8	POLR2A	chr4:48018435-48018980	H1-hESC	embryonic stem cell:	n/a	n/a
9	RCOR1	chr4:48018237-48018639	K562	blood:	n/a	n/a
10	POLR2A	chr4:48018541-48018855	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr4:48018466-48018927	GM12891	blood:	n/a	n/a
12	POLR2A	chr4:48018512-48018944	HUVEC	blood vessel:	n/a	n/a
13	E2F6	chr4:48018272-48019360	H1-hESC	embryonic stem cell:	n/a	chr4:48018748-48018762 chr4:48018778-48018787 chr4:48018739-48018748
14	TBL1XR1	chr4:48018375-48018725	GM12878	blood:	n/a	n/a
15	PAX5	chr4:48018381-48018949	GM12892	blood:	n/a	n/a
16	TAF1	chr4:48018344-48018958	H1-hESC	embryonic stem cell:	n/a	n/a
17	ZBTB7A	chr4:48018574-48018942	K562	blood:	n/a	chr4:48018646-48018654
18	RAD21	chr4:48018175-48018657	HepG2	liver:	n/a	chr4:48018447-48018466
19	STAT5A	chr4:48018321-48018627	GM12878	blood:	n/a	chr4:48018481-48018501
20	MYC	chr4:48018503-48019580	MCF10A-Er-Src	breast:	n/a	chr4:48019432-48019441 chr4:48019176-48019183
21	RAD21	chr4:48018175-48018657	ECC-1	luminal epithelium:	n/a	chr4:48018447-48018466
22	CEBPD	chr4:48018376-48018957	HepG2	liver:	n/a	n/a
23	RFX5	chr4:48018356-48019298	Hela-S3	cervix:	n/a	n/a
24	TCF12	chr4:48018136-48019597	ECC-1	luminal epithelium:	n/a	chr4:48018588-48018598
25	SETDB1	chr4:48018229-48018666	U2OS	brain:	n/a	n/a
26	POLR2A	chr4:48018308-48018991	GM12878	blood:	n/a	n/a
27	BCLAF1	chr4:48018183-48019163	GM12878	blood:	n/a	chr4:48018766-48018779 chr4:48018770-48018783
28	POLR2A	chr4:48018557-48018674	Gliobla	brain:	n/a	n/a
29	TFAP2C	chr4:48018288-48019589	Hela-S3	cervix:	n/a	n/a
30	TBP	chr4:48018507-48018947	K562	blood:	n/a	n/a
31	CTBP2	chr4:48018238-48019635	H1-hESC	embryonic stem cell:	n/a	n/a
32	CHD2	chr4:48018411-48018918	HepG2	liver:	n/a	n/a
33	MAZ	chr4:48018275-48019179	Hela-S3	cervix:	n/a	n/a
34	YY1	chr4:48018420-48019063	HepG2	liver:	n/a	chr4:48018730-48018744 chr4:48018739-48018748 chr4:48018770-48018781
35	POLR2A	chr4:48018332-48018941	H1-hESC	embryonic stem cell:	n/a	n/a
36	ELF1	chr4:48018557-48018921	K562	blood:	n/a	n/a
37	STAT5A	chr4:48018104-48018656	GM12878	blood:	n/a	chr4:48018112-48018119 chr4:48018481-48018501 chr4:48018105-48018119
38	POLR2A	chr4:48018461-48019264	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr4:48018126-48018765	K562	blood:	n/a	n/a
40	MAX	chr4:48018280-48019499	MCF-7	breast:	n/a	chr4:48019432-48019441 chr4:48019176-48019183
41	CTCF	chr4:48018283-48018618	GM19238	blood:	n/a	n/a
42	TCF7L2	chr4:48018232-48018684	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr4:48018575-48018701	A549	lung:	n/a	n/a
44	CEBPB	chr4:48018370-48018651	H1-hESC	embryonic stem cell:	n/a	n/a
45	NFATC1	chr4:48018242-48018640	GM12878	blood:	n/a	n/a
46	CTCF	chr4:48018241-48018653	K562	blood:	n/a	n/a
47	CTCF	chr4:48017913-48019455	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr4:48018466-48018952	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr4:48018327-48019709	ECC-1	luminal epithelium:	n/a	n/a
50	MYC	chr4:48018460-48018663	MCF-7	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:48018582-48018632	SK-N-SH_RA	brain:	n/a
2	chr4:48018582-48018632	AG09319	gingival:	n/a
3	chr4:48018582-48018632	Hela-S3	cervix:	n/a
4	chr4:48018582-48018632	ECC-1	luminal epithelium:	n/a
5	chr4:48018582-48018632	HMEC	breast:	n/a
6	chr4:48018582-48018632	HUVEC	blood vessel:	n/a
7	chr4:48018582-48018632	SKMC	muscle:	n/a
8	chr4:48018582-48018632	HepG2	liver:	n/a
9	chr4:48018582-48018632	HRPEpiC	eye:	n/a
10	chr4:48018582-48018632	BE2_C	brain:	n/a
11	chr4:48018582-48018632	GM12892	blood:	n/a
12	chr4:48018582-48018632	U87	brain:	n/a
13	chr4:48018582-48018632	MCF-7	breast:	n/a
14	chr4:48018582-48018632	HPAEpiC	pulmonary alveolar:	n/a
15	chr4:48018582-48018632	ProgFib	skin:	n/a
16	chr4:48018582-48018632	NHDF-neo	bronchial:	n/a
17	chr4:48018582-48018632	SK-N-SH	brain:	n/a
18	chr4:48018582-48018632	GM12878	blood:	n/a
19	chr4:48018582-48018632	HIPEpiC	eye:	n/a
20	chr4:48018582-48018632	PFSK-1	brain:	n/a
21	chr4:48018582-48018632	MCF10A-Er-Src	breast:	n/a
22	chr4:48018582-48018632	NB4	blood:	n/a
23	chr4:48018582-48018632	PANC-1	pancreas:	n/a
24	chr4:48018582-48018632	HAEpiC	amniotic membrane:	n/a
25	chr4:48018582-48018632	NHBE	bronchial:	n/a
26	chr4:48018582-48018632	AG09309	skin:	n/a
27	chr4:48018582-48018632	ovcar-3	ovarian:	n/a
28	chr4:48018582-48018632	RPTEC	kidney:	n/a
29	chr4:48018582-48018632	Caco-2	colon:	n/a
30	chr4:48018582-48018632	Hepatocyte	liver:	n/a
31	chr4:48018582-48018632	Jurkat	blood:	n/a
32	chr4:48018582-48018632	NT2-D1	testis:	n/a
33	chr4:48018582-48018632	HEEpiC	esophagus:	n/a
34	chr4:48018582-48018632	HCM	heart:	n/a
35	chr4:48018582-48018632	HCT-116	colon:	n/a
36	chr4:48018582-48018632	IMR90	lung:	fetal
37	chr4:48018582-48018632	HL-60	blood:	n/a
38	chr4:48018582-48018632	HRE	kidney:	n/a
39	chr4:48018582-48018632	GM12891	blood:	n/a
40	chr4:48018582-48018632	SAEC	small airway:	n/a
41	chr4:48018582-48018632	BJ	skin:	n/a
42	chr4:48018582-48018632	HNPCEpiC	eye:	n/a
43	chr4:48018582-48018632	K562	blood:	n/a
44	chr4:48018582-48018632	AG04449	skin:	fetal
45	chr4:48018582-48018632	AoSMC	blood vessel:	n/a
46	chr4:48018582-48018632	AG10803	skin:	n/a
47	chr4:48018582-48018632	NH-A	brain:	n/a
48	chr4:48018582-48018632	SK-N-MC	brain:	n/a
49	chr4:48018582-48018632	PrEC	prostate:	n/a
50	chr4:48018582-48018632	HCF	heart:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:47915045..47916605-chr4:48017433..48018940,2	MCF-7	breast:
2	chr4:47914296..47917191-chr4:48017364..48021197,5	MCF-7	breast:
3	chr4:48018226..48018849-chr5:157285675..157286547,2	HCT-116	colon:

No data

Variant related genes	Relation type
NIPAL1	TF binding region
CNGA1	TF binding region
NIPAL1	CpG island
CNGA1	CpG island
ENSG00000163293	Chromatin interaction
ENSG00000113282	Chromatin interaction
ENSG00000170448	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs13116684	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13121957	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13140968	0.81[AFR][1000 genomes]
rs13145218	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13150783	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13151608	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs224799	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs321622	0.83[AFR][1000 genomes]
rs321628	0.94[AFR][1000 genomes]
rs321630	0.94[AFR][1000 genomes]
rs321631	0.94[AFR][1000 genomes]
rs321632	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs321635	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	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55670663	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6447609	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6812991	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7674929	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs98270	0.95[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
rs321634	CNGA1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48017400-48019200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr4:48017400-48020200	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr4:48017600-48019000	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr4:48017600-48019000	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr4:48017600-48019200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr4:48017600-48020600	Active TSS	Rectal Smooth Muscle	rectum
7	chr4:48017800-48018800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:48017800-48019000	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr4:48017800-48019200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:48017800-48019600	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr4:48017800-48019800	Active TSS	Esophagus	oesophagus
12	chr4:48017800-48019800	Active TSS	Fetal Kidney	kidney
13	chr4:48018000-48018800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:48018000-48018800	Active TSS	Fetal Intestine Small	intestine
15	chr4:48018000-48019000	Active TSS	H1 Cell Line	embryonic stem cell
16	chr4:48018000-48019000	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr4:48018000-48019400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr4:48018000-48019400	Active TSS	Fetal Heart	heart
19	chr4:48018000-48019400	Active TSS	A549	lung
20	chr4:48018000-48019600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:48018000-48019600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:48018000-48019600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:48018000-48019600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr4:48018000-48019600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
25	chr4:48018000-48019600	Active TSS	Brain Substantia Nigra	brain
26	chr4:48018000-48019600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
27	chr4:48018000-48019600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
28	chr4:48018000-48019800	Active TSS	H9 Cell Line	embryonic stem cell
29	chr4:48018000-48019800	Active TSS	NH-A	brain
30	chr4:48018000-48020000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:48018000-48020400	Active TSS	Duodenum Mucosa	Duodenum
32	chr4:48018000-48020600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:48018200-48018800	Active TSS	Muscle Satellite Cultured Cells	--
34	chr4:48018200-48018800	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr4:48018200-48018800	Active TSS	HSMM	muscle
36	chr4:48018200-48018800	Active TSS	NHDF-Ad	bronchial
37	chr4:48018200-48018800	Active TSS	NHLF	lung
38	chr4:48018200-48019000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:48018200-48019000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:48018200-48019000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:48018200-48019000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr4:48018200-48019000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr4:48018200-48019000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:48018200-48019000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr4:48018200-48019000	Active TSS	Brain Angular Gyrus	brain
46	chr4:48018200-48019000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr4:48018200-48019000	Active TSS	GM12878-XiMat	blood
48	chr4:48018200-48019200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
49	chr4:48018200-48019200	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
50	chr4:48018200-48019400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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