Variant report

Variant	rs563543643
Chromosome Location	chr1:228756825-228756826
allele	A/C
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	REST	chr1:228756787-228757408	SK-N-SH	brain:	n/a	n/a
2	SPI1	chr1:228756749-228756880	K562	blood:	n/a	n/a
3	POLR2A	chr1:228756767-228756963	Hela-S3	cervix:	n/a	n/a
4	ZBTB7A	chr1:228756683-228756860	HepG2	liver:	n/a	n/a
5	ZBTB33	chr1:228756674-228756910	K562	blood:	n/a	n/a
6	FOSL2	chr1:228756617-228756913	HepG2	liver:	n/a	n/a
7	TCF3	chr1:228756566-228756927	GM12878	blood:	n/a	n/a
8	TEAD4	chr1:228756658-228757548	HepG2	liver:	n/a	n/a
9	SPI1	chr1:228756688-228756899	GM12878	blood:	n/a	n/a
10	SIN3AK20	chr1:228756514-228757466	A549	lung:	n/a	n/a
11	CHD2	chr1:228756766-228756968	HepG2	liver:	n/a	n/a
12	MAX	chr1:228756771-228756971	HepG2	liver:	n/a	n/a
13	HEY1	chr1:228756583-228756919	HepG2	liver:	n/a	chr1:228756662-228756677 chr1:228756751-228756766 chr1:228756754-228756769
14	IRF4	chr1:228756684-228756919	GM12878	blood:	n/a	n/a
15	PAX5	chr1:228756690-228756905	GM12878	blood:	n/a	n/a
16	SP1	chr1:228756695-228756932	GM12878	blood:	n/a	n/a
17	TCF12	chr1:228756706-228756896	GM12878	blood:	n/a	n/a
18	CEBPD	chr1:228756659-228756869	HepG2	liver:	n/a	n/a
19	USF1	chr1:228756716-228756889	HepG2	liver:	n/a	chr1:228756750-228756766 chr1:228756755-228756771
20	SIN3AK20	chr1:228756615-228758936	A549	lung:	n/a	n/a
21	ZBTB33	chr1:228756665-228756921	K562	blood:	n/a	n/a
22	POLR2A	chr1:228743903-228763119	PANC-1	pancreas:	n/a	n/a
23	TCF12	chr1:228756702-228756908	GM12878	blood:	n/a	n/a
24	EBF1	chr1:228756714-228756901	GM12878	blood:	n/a	n/a
25	SIX5	chr1:228756691-228756915	K562	blood:	n/a	n/a
26	BCL11A	chr1:228756724-228756902	GM12878	blood:	n/a	chr1:228756756-228756769 chr1:228756760-228756769 chr1:228756837-228756850 chr1:228756750-228756763 chr1:228756749-228756762
27	CHD2	chr1:228756661-228756864	Hela-S3	cervix:	n/a	n/a
28	JUND	chr1:228744099-228759006	A549	lung:	n/a	chr1:228748791-228748805 chr1:228747728-228747737 chr1:228753273-228753287 chr1:228744309-228744323 chr1:228746550-228746564 chr1:228745487-228745496 chr1:228755514-228755528 chr1:228751032-228751046 chr1:228758886-228758895 chr1:228749969-228749978 chr1:228752210-228752219 chr1:228754451-228754460 chr1:228757729-228757743
29	ZBTB33	chr1:228756695-228756929	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:228756571-228757031	HepG2	liver:	n/a	n/a
31	SP1	chr1:228756690-228756929	GM12878	blood:	n/a	n/a
32	SIN3AK20	chr1:228756724-228756879	HepG2	liver:	n/a	n/a
33	MYBL2	chr1:228756642-228757571	HepG2	liver:	n/a	n/a
34	PBX3	chr1:228756735-228756888	GM12878	blood:	n/a	n/a
35	YY1	chr1:228756712-228758545	A549	lung:	n/a	chr1:228756750-228756764 chr1:228756760-228756771 chr1:228756754-228756765 chr1:228757396-228757405 chr1:228757394-228757405 chr1:228757810-228757819 chr1:228756747-228756758
36	JUND	chr1:228756630-228756893	HepG2	liver:	n/a	n/a
37	FOXA2	chr1:228743895-228782766	A549	lung:	n/a	n/a
38	PAX5	chr1:228756585-228756945	GM12878	blood:	n/a	n/a
39	POLR2A	chr1:228752325-228758678	SK-N-MC	brain:	n/a	n/a
40	EP300	chr1:228756748-228756900	GM12878	blood:	n/a	n/a
41	CTCF	chr1:228756680-228756830	BE2_C	brain:	n/a	n/a
42	FOXM1	chr1:228756691-228757384	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:228743920-228757394	PFSK-1	brain:	n/a	n/a
44	SIX5	chr1:228743910-228770094	A549	lung:	n/a	n/a
45	CBX3	chr1:228756716-228760610	K562	blood:	n/a	n/a
46	ZBTB33	chr1:228756693-228756945	GM12878	blood:	n/a	n/a
47	POU2F2	chr1:228756659-228756932	GM12878	blood:	n/a	chr1:228756757-228756769
48	HCFC1	chr1:228756677-228756907	Hela-S3	cervix:	n/a	n/a
49	MYBL2	chr1:228756565-228759813	HepG2	liver:	n/a	n/a
50	POU2F2	chr1:228756742-228756876	GM12878	blood:	n/a	chr1:228756757-228756769

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:228756789-228756839	HUVEC	blood vessel:	n/a
2	chr1:228756789-228756839	NT2-D1	testis:	n/a
3	chr1:228756789-228756839	A549	lung:	n/a
4	chr1:228756789-228756839	HEK293	kidney:	embryo
5	chr1:228756789-228756839	MCF10A-Er-Src	breast:	n/a
6	chr1:228756789-228756839	Hela-S3	cervix:	n/a
7	chr1:228756789-228756839	SK-N-MC	brain:	n/a
8	chr1:228756789-228756839	HEEpiC	esophagus:	n/a
9	chr1:228756789-228756839	HAEpiC	amniotic membrane:	n/a
10	chr1:228756789-228756839	IMR90	lung:	fetal
11	chr1:228756789-228756839	SKMC	muscle:	n/a
12	chr1:228756789-228756839	HepG2	liver:	n/a
13	chr1:228756789-228756839	Jurkat	blood:	n/a
14	chr1:228756789-228756839	HRCEpiC	kidney:	n/a
15	chr1:228756789-228756839	HCT-116	colon:	n/a
16	chr1:228756789-228756839	ProgFib	skin:	n/a
17	chr1:228756789-228756839	HMEC	breast:	n/a
18	chr1:228756789-228756839	HIPEpiC	eye:	n/a
19	chr1:228756789-228756839	AG10803	skin:	n/a
20	chr1:228756789-228756839	HRE	kidney:	n/a
21	chr1:228756789-228756839	BE2_C	brain:	n/a
22	chr1:228756789-228756839	GM12878	blood:	n/a
23	chr1:228756789-228756839	MCF-7	breast:	n/a
24	chr1:228756789-228756839	PANC-1	pancreas:	n/a
25	chr1:228756789-228756839	K562	blood:	n/a
26	chr1:228756789-228756839	NHBE	bronchial:	n/a
27	chr1:228756789-228756839	Caco-2	colon:	n/a
28	chr1:228756789-228756839	AG04449	skin:	fetal
29	chr1:228756789-228756839	GM19239	blood:	n/a
30	chr1:228756789-228756839	CMK	blood:	n/a
31	chr1:228756789-228756839	PFSK-1	brain:	n/a
32	chr1:228756789-228756839	HCF	heart:	n/a
33	chr1:228756789-228756839	HPAEpiC	pulmonary alveolar:	n/a
34	chr1:228756789-228756839	HNPCEpiC	eye:	n/a
35	chr1:228756789-228756839	AG09319	gingival:	n/a
36	chr1:228756789-228756839	AG09309	skin:	n/a
37	chr1:228756789-228756839	BJ	skin:	n/a
38	chr1:228756789-228756839	HCM	heart:	n/a
39	chr1:228756789-228756839	GM06990	blood:	n/a
40	chr1:228756789-228756839	NHDF-neo	bronchial:	n/a
41	chr1:228756789-228756839	NH-A	brain:	n/a
42	chr1:228756789-228756839	PrEC	prostate:	n/a
43	chr1:228756789-228756839	T-47D	breast:	n/a
44	chr1:228756789-228756839	AG04450	lung:	fetal
45	chr1:228756789-228756839	U87	brain:	n/a
46	chr1:228756789-228756839	HRPEpiC	eye:	n/a
47	chr1:228756789-228756839	SK-N-SH	brain:	n/a
48	chr1:228756789-228756839	LNCaP	prostate:	n/a
49	chr1:228756789-228756839	SK-N-SH_RA	brain:	n/a
50	chr1:228756789-228756839	H1-hESC	embryonic stem cell:	embryo

Variant related genes	Relation type
RNA5S4	TF binding region
RNA5S5	TF binding region
RNA5S4	CpG island
RNA5S5	CpG island

Extended variants
information (count: 20 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv827075	chr1:228716554-228783674	Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
4	nsv945355	chr1:228716611-228784016	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	29 gene(s)	inside rSNPs	diseases
5	nsv511124	chr1:228742457-228780671	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island	18 gene(s)	inside rSNPs	diseases
6	esv19715	chr1:228742638-228783674	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
7	esv3425415	chr1:228742829-228783527	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
8	nsv827086	chr1:228742962-228783035	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
9	nsv820567	chr1:228742962-228783403	Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
10	nsv827097	chr1:228742962-228783403	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
11	esv3331974	chr1:228743029-228783527	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
12	esv3342484	chr1:228743029-228783527	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
13	esv3382956	chr1:228743029-228783527	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
14	esv3445359	chr1:228743029-228783527	Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
15	esv3450984	chr1:228743029-228783527	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
16	esv1816306	chr1:228743784-228781208	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island	17 gene(s)	inside rSNPs	diseases
17	esv1823022	chr1:228744778-228780896	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island	17 gene(s)	inside rSNPs	diseases
18	esv1849885	chr1:228744778-228780896	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island	17 gene(s)	inside rSNPs	diseases
19	nsv160307	chr1:228755737-228757939	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
20	nsv159946	chr1:228755745-228757939	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228756600-228757000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:228756600-228757000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:228756600-228757000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:228756600-228757000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:228756600-228757000	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr1:228756600-228757000	Enhancers	Primary B cells from peripheral blood	blood
7	chr1:228756600-228757000	Active TSS	Primary T cells from cord blood	blood
8	chr1:228756600-228757000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr1:228756600-228757000	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr1:228756600-228757000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:228756600-228757000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:228756600-228757000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:228756600-228757000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:228756600-228757000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:228756600-228757000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:228756600-228757000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
17	chr1:228756600-228757000	Active TSS	Brain Angular Gyrus	brain
18	chr1:228756600-228757000	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr1:228756600-228757000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
20	chr1:228756600-228757000	ZNF genes & repeats	Esophagus	oesophagus
21	chr1:228756600-228757000	Bivalent Enhancer	Fetal Brain Male	brain
22	chr1:228756600-228757000	Flanking Bivalent TSS/Enh	Lung	lung
23	chr1:228756600-228757000	Flanking Bivalent TSS/Enh	Ovary	ovary
24	chr1:228756600-228757000	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
25	chr1:228756600-228757000	ZNF genes & repeats	Right Atrium	heart
26	chr1:228756600-228757000	Flanking Bivalent TSS/Enh	Right Ventricle	heart
27	chr1:228756600-228757000	Flanking Bivalent TSS/Enh	Sigmoid Colon	Sigmoid Colon
28	chr1:228756600-228757000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
29	chr1:228756600-228757000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
30	chr1:228756600-228757000	Flanking Bivalent TSS/Enh	Thymus	Thymus
31	chr1:228756600-228757000	Active TSS	HepG2	liver
32	chr1:228756800-228757000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
33	chr1:228756800-228757000	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
34	chr1:228756800-228757000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
35	chr1:228756800-228757000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
36	chr1:228756800-228757000	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
37	chr1:228756800-228757000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr1:228756800-228757000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
39	chr1:228756800-228757000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:228756800-228757000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:228756800-228757000	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
42	chr1:228756800-228757000	Flanking Active TSS	Brain Hippocampus Middle	brain
43	chr1:228756800-228757000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr1:228756800-228757000	Flanking Bivalent TSS/Enh	Fetal Lung	lung
45	chr1:228756800-228757000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
46	chr1:228756800-228757000	Bivalent Enhancer	Fetal Muscle Leg	muscle
47	chr1:228756800-228757000	Bivalent Enhancer	Fetal Stomach	stomach
48	chr1:228756800-228757000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
49	chr1:228756800-228757000	Bivalent/Poised TSS	Left Ventricle	heart
50	chr1:228756800-228757000	Flanking Bivalent TSS/Enh	Small Intestine	intestine

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