Variant report

Variant	rs563554466
Chromosome Location	chr1:224179857-224179858
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	POLR2A	chr1:224179744-224180784	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr1:224179691-224180920	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:224178488-224181742	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZBTB33	chr1:224179748-224180307	K562	blood:	n/a	n/a
5	SIX5	chr1:224179719-224180580	K562	blood:	n/a	n/a
6	NFIC	chr1:224179796-224180591	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:224178929-224180943	GM12892	blood:	n/a	n/a
8	TAF1	chr1:224179838-224180875	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:224179842-224181001	U87	brain:	n/a	n/a
10	GATA2	chr1:224179742-224180837	K562	blood:	n/a	n/a
11	BATF	chr1:224179785-224180831	GM12878	blood:	n/a	n/a
12	POU2F2	chr1:224179792-224180888	GM12878	blood:	n/a	n/a
13	SP1	chr1:224179799-224180916	GM12878	blood:	n/a	chr1:224180308-224180319 chr1:224180399-224180420
14	IRF4	chr1:224179738-224180902	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:224178787-224181394	GM12892	blood:	n/a	n/a
16	NR2F2	chr1:224179427-224181073	K562	blood:	n/a	n/a
17	FOSL2	chr1:224179653-224180880	HepG2	liver:	n/a	chr1:224180402-224180411 chr1:224180345-224180354
18	POLR2A	chr1:224179402-224181020	H1-hESC	embryonic stem cell:	n/a	n/a
19	HEY1	chr1:224179277-224181085	HepG2	liver:	n/a	chr1:224180346-224180355 chr1:224180089-224180104 chr1:224180344-224180353 chr1:224180528-224180543 chr1:224180722-224180737
20	YY1	chr1:224179755-224180884	A549	lung:	n/a	chr1:224180529-224180540 chr1:224180713-224180727 chr1:224180526-224180537 chr1:224180532-224180541 chr1:224180700-224180714 chr1:224180052-224180060
21	PAX5	chr1:224179728-224181406	GM12878	blood:	n/a	n/a
22	TAF1	chr1:224179848-224181013	H1-hESC	embryonic stem cell:	n/a	n/a
23	HEY1	chr1:224178955-224180994	K562	blood:	n/a	chr1:224180346-224180355 chr1:224180089-224180104 chr1:224180344-224180353 chr1:224180528-224180543 chr1:224180722-224180737
24	CEBPB	chr1:224179718-224180685	K562	blood:	n/a	chr1:224180401-224180409
25	REST	chr1:224179855-224180848	SK-N-SH	brain:	n/a	chr1:224180245-224180255 chr1:224180725-224180743 chr1:224180701-224180714
26	POLR2A	chr1:224179703-224180938	Hela-S3	cervix:	n/a	n/a
27	SIN3AK20	chr1:224179764-224180969	HepG2	liver:	n/a	n/a
28	BCL11A	chr1:224179801-224179949	GM12878	blood:	n/a	n/a
29	PAX5	chr1:224179228-224181319	GM12878	blood:	n/a	n/a
30	ZBTB33	chr1:224179850-224180883	GM12878	blood:	n/a	n/a
31	HEY1	chr1:224178879-224180994	K562	blood:	n/a	chr1:224180346-224180355 chr1:224180089-224180104 chr1:224180344-224180353 chr1:224180528-224180543 chr1:224180722-224180737
32	POLR2A	chr1:224178883-224181083	GM12878	blood:	n/a	n/a
33	CTCF	chr1:224179325-224181033	K562	blood:	n/a	n/a
34	POLR2A	chr1:224179362-224181605	PFSK-1	brain:	n/a	n/a
35	POLR2A	chr1:224178829-224181509	GM12892	blood:	n/a	n/a
36	POLR2A	chr1:224179005-224180945	GM12891	blood:	n/a	n/a
37	POU2F2	chr1:224178930-224181599	GM12878	blood:	n/a	n/a
38	TAF1	chr1:224179832-224180842	GM12891	blood:	n/a	n/a
39	TAF1	chr1:224179415-224181129	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr1:224178915-224181048	GM12892	blood:	n/a	n/a
41	SPI1	chr1:224179854-224180040	K562	blood:	n/a	n/a
42	POLR2A	chr1:224179271-224181047	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr1:224179743-224180838	HepG2	liver:	n/a	n/a
44	TCF3	chr1:224179848-224180916	GM12878	blood:	n/a	chr1:224180643-224180653 chr1:224180645-224180658
45	MYBL2	chr1:224179808-224180714	HepG2	liver:	n/a	n/a
46	TAF1	chr1:224179844-224180953	GM12891	blood:	n/a	n/a
47	POLR2A	chr1:224179702-224180911	A549	lung:	n/a	n/a
48	TAF1	chr1:224179793-224180901	GM12878	blood:	n/a	n/a
49	TAF1	chr1:224179828-224180892	Hela-S3	cervix:	n/a	n/a
50	TAF1	chr1:224179838-224180962	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:223887763..223889342-chr1:224178879..224180474,2	K562	blood:
2	chr1:224178733..224180652-chr1:224310129..224312087,2	K562	blood:
3	chr1:224178905..224181889-chr1:224301318..224303879,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243000	TF binding region
ENSG00000185495	TF binding region
ENSG00000232372	TF binding region
ENSG00000162909	Chromatin interaction
ENSG00000143756	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv873215	chr1:224075483-224204433	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv873216	chr1:224075483-224230307	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv1802502	chr1:224076065-224184733	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv427941	chr1:224085052-224363163	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv873217	chr1:224089383-224190316	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv15701	chr1:224096726-224179951	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv873218	chr1:224097155-224204433	Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv873219	chr1:224097155-224216822	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv873220	chr1:224097155-224223659	ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv549241	chr1:224103992-224216757	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv873221	chr1:224115297-224183599	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv549242	chr1:224115297-224203918	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv549243	chr1:224115297-224216757	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv945316	chr1:224133366-224196526	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
17	nsv947070	chr1:224178779-224183075	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224176000-224180000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:224179000-224182200	Active TSS	GM12878-XiMat	blood
3	chr1:224179200-224181800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:224179400-224181400	Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr1:224179400-224182200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:224179600-224180000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr1:224179600-224180000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr1:224179600-224181400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:224179600-224181400	Active TSS	Brain Hippocampus Middle	brain
10	chr1:224179600-224181400	Active TSS	Fetal Muscle Leg	muscle
11	chr1:224179600-224181400	Active TSS	Dnd41	blood
12	chr1:224179600-224181400	Active TSS	NHEK	skin
13	chr1:224179600-224181600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:224179600-224181600	Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr1:224179600-224181600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:224179600-224181600	Active TSS	Brain Angular Gyrus	brain
17	chr1:224179600-224181600	Active TSS	Fetal Intestine Large	intestine
18	chr1:224179600-224181600	Active TSS	A549	lung
19	chr1:224179600-224181600	Active TSS	HMEC	breast
20	chr1:224179600-224181600	Active TSS	HSMM	muscle
21	chr1:224179600-224181600	Active TSS	K562	blood
22	chr1:224179600-224181800	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr1:224179600-224181800	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr1:224179600-224181800	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr1:224179600-224181800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:224179600-224181800	Active TSS	Fetal Intestine Small	intestine
27	chr1:224179600-224181800	Active TSS	Stomach Smooth Muscle	stomach
28	chr1:224179600-224182200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:224179600-224182200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:224179600-224182200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:224179600-224182200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:224179600-224182200	Active TSS	Osteobl	bone
33	chr1:224179600-224182400	Active TSS	HepG2	liver
34	chr1:224179800-224180000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:224179800-224181000	Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr1:224179800-224181000	Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr1:224179800-224181000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:224179800-224181200	Active TSS	Primary B cells from peripheral blood	blood
39	chr1:224179800-224181200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr1:224179800-224181200	Active TSS	Psoas Muscle	Psoas
41	chr1:224179800-224181400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:224179800-224181400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:224179800-224181400	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr1:224179800-224181400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:224179800-224181400	Active TSS	Primary T cells from cord blood	blood
46	chr1:224179800-224181400	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr1:224179800-224181400	Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr1:224179800-224181400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:224179800-224181400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr1:224179800-224181400	Active TSS	Primary T killer naive cells fromperipheralblood	blood

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