Variant report

Variant	rs540605093
Chromosome Location	chr1:224179691-224179692
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:224179691-224180920	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:224178488-224181742	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr1:224179400-224179700	K562	blood:	n/a	n/a
4	POLR2A	chr1:224178929-224180943	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:224178787-224181394	GM12892	blood:	n/a	n/a
6	NR2F2	chr1:224179427-224181073	K562	blood:	n/a	n/a
7	FOSL2	chr1:224179653-224180880	HepG2	liver:	n/a	chr1:224180402-224180411 chr1:224180345-224180354
8	POLR2A	chr1:224179402-224181020	H1-hESC	embryonic stem cell:	n/a	n/a
9	HEY1	chr1:224179277-224181085	HepG2	liver:	n/a	chr1:224180346-224180355 chr1:224180089-224180104 chr1:224180344-224180353 chr1:224180528-224180543 chr1:224180722-224180737
10	HEY1	chr1:224178955-224180994	K562	blood:	n/a	chr1:224180346-224180355 chr1:224180089-224180104 chr1:224180344-224180353 chr1:224180528-224180543 chr1:224180722-224180737
11	PAX5	chr1:224179228-224181319	GM12878	blood:	n/a	n/a
12	HEY1	chr1:224178879-224180994	K562	blood:	n/a	chr1:224180346-224180355 chr1:224180089-224180104 chr1:224180344-224180353 chr1:224180528-224180543 chr1:224180722-224180737
13	CTCF	chr1:224179412-224179726	K562	blood:	n/a	n/a
14	POLR2A	chr1:224178883-224181083	GM12878	blood:	n/a	n/a
15	CTCF	chr1:224179325-224181033	K562	blood:	n/a	n/a
16	POLR2A	chr1:224179362-224181605	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr1:224178829-224181509	GM12892	blood:	n/a	n/a
18	POLR2A	chr1:224179005-224180945	GM12891	blood:	n/a	n/a
19	POU2F2	chr1:224178930-224181599	GM12878	blood:	n/a	n/a
20	CBX3	chr1:224179390-224179770	K562	blood:	n/a	n/a
21	TAF1	chr1:224179415-224181129	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr1:224178915-224181048	GM12892	blood:	n/a	n/a
23	POLR2A	chr1:224179271-224181047	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr1:224179580-224179730	K562	blood:	n/a	n/a
25	POLR2A	chr1:224179002-224180944	GM12878	blood:	n/a	n/a
26	POLR2A	chr1:224178995-224180868	GM12891	blood:	n/a	n/a
27	POLR2A	chr1:224178716-224181850	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr1:224179678-224180890	H1-hESC	embryonic stem cell:	n/a	n/a
29	POU2F2	chr1:224179004-224180914	GM12891	blood:	n/a	n/a
30	POLR2A	chr1:224178738-224182255	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:224179540-224179765	K562	blood:	n/a	n/a
32	POLR2A	chr1:224178886-224181322	GM12891	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:224179665-224179715	BE2_C	brain:	n/a
2	chr1:224179665-224179715	PANC-1	pancreas:	n/a
3	chr1:224179665-224179715	GM12878	blood:	n/a
4	chr1:224179665-224179715	MCF-7	breast:	n/a
5	chr1:224179665-224179715	HAEpiC	amniotic membrane:	n/a
6	chr1:224179665-224179715	RPTEC	kidney:	n/a
7	chr1:224179665-224179715	AG04449	skin:	fetal
8	chr1:224179665-224179715	AG09319	gingival:	n/a
9	chr1:224179665-224179715	NH-A	brain:	n/a
10	chr1:224179665-224179715	MCF10A-Er-Src	breast:	n/a
11	chr1:224179665-224179715	PFSK-1	brain:	n/a
12	chr1:224179665-224179715	Hela-S3	cervix:	n/a
13	chr1:224179665-224179715	Jurkat	blood:	n/a
14	chr1:224179665-224179715	T-47D	breast:	n/a
15	chr1:224179665-224179715	NHBE	bronchial:	n/a
16	chr1:224179665-224179715	HCPEpiC	choroid plexus:	n/a
17	chr1:224179665-224179715	AG09309	skin:	n/a
18	chr1:224179665-224179715	HEEpiC	esophagus:	n/a
19	chr1:224179665-224179715	GM12891	blood:	n/a
20	chr1:224179665-224179715	GM12892	blood:	n/a
21	chr1:224179665-224179715	SAEC	small airway:	n/a
22	chr1:224179665-224179715	HRCEpiC	kidney:	n/a
23	chr1:224179665-224179715	ProgFib	skin:	n/a
24	chr1:224179665-224179715	GM06990	blood:	n/a
25	chr1:224179665-224179715	ECC-1	luminal epithelium:	n/a
26	chr1:224179665-224179715	HCT-116	colon:	n/a
27	chr1:224179665-224179715	K562	blood:	n/a
28	chr1:224179665-224179715	BJ	skin:	n/a
29	chr1:224179665-224179715	HCF	heart:	n/a
30	chr1:224179665-224179715	AoSMC	blood vessel:	n/a
31	chr1:224179665-224179715	HRE	kidney:	n/a
32	chr1:224179665-224179715	NB4	blood:	n/a
33	chr1:224179665-224179715	AG04450	lung:	fetal
34	chr1:224179665-224179715	SK-N-MC	brain:	n/a
35	chr1:224179665-224179715	CMK	blood:	n/a
36	chr1:224179665-224179715	HIPEpiC	eye:	n/a
37	chr1:224179665-224179715	SK-N-SH	brain:	n/a
38	chr1:224179665-224179715	SK-N-SH_RA	brain:	n/a
39	chr1:224179665-224179715	U87	brain:	n/a
40	chr1:224179665-224179715	H1-hESC	embryonic stem cell:	embryo
41	chr1:224179665-224179715	IMR90	lung:	fetal
42	chr1:224179665-224179715	A549	lung:	n/a
43	chr1:224179665-224179715	HUVEC	blood vessel:	n/a
44	chr1:224179665-224179715	HL-60	blood:	n/a
45	chr1:224179665-224179715	AG10803	skin:	n/a
46	chr1:224179665-224179715	HNPCEpiC	eye:	n/a
47	chr1:224179665-224179715	Caco-2	colon:	n/a
48	chr1:224179665-224179715	LNCaP	prostate:	n/a
49	chr1:224179665-224179715	NT2-D1	testis:	n/a
50	chr1:224179665-224179715	Hepatocyte	liver:	n/a

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

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:

No data

Variant related genes	Relation type
ENSG00000232372	TF binding region
ENSG00000243000	TF binding region
ENSG00000185495	TF binding region
ENSG00000243000	CpG island
ENSG00000185495	CpG island
ENSG00000232372	CpG island
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:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224136400-224179800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:224138400-224179800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr1:224138800-224179800	Weak transcription	Left Ventricle	heart
4	chr1:224140200-224179800	Weak transcription	Placenta	Placenta
5	chr1:224140400-224179800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:224145000-224179800	Weak transcription	Primary T cells from cord blood	blood
7	chr1:224150000-224179800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:224150000-224179800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:224150200-224179800	Weak transcription	Liver	Liver
10	chr1:224158000-224179800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:224161600-224179800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:224168800-224179800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:224173600-224179800	Weak transcription	Fetal Stomach	stomach
14	chr1:224176000-224180000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:224179000-224182200	Active TSS	GM12878-XiMat	blood
16	chr1:224179200-224179800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:224179200-224181800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:224179400-224179800	Weak transcription	Psoas Muscle	Psoas
19	chr1:224179400-224179800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:224179400-224181400	Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr1:224179400-224182200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:224179600-224179800	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr1:224179600-224179800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:224179600-224179800	Weak transcription	Brain Anterior Caudate	brain
25	chr1:224179600-224179800	Weak transcription	Pancreas	Pancrea
26	chr1:224179600-224179800	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr1:224179600-224180000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr1:224179600-224180000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
29	chr1:224179600-224181400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:224179600-224181400	Active TSS	Brain Hippocampus Middle	brain
31	chr1:224179600-224181400	Active TSS	Fetal Muscle Leg	muscle
32	chr1:224179600-224181400	Active TSS	Dnd41	blood
33	chr1:224179600-224181400	Active TSS	NHEK	skin
34	chr1:224179600-224181600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:224179600-224181600	Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr1:224179600-224181600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:224179600-224181600	Active TSS	Brain Angular Gyrus	brain
38	chr1:224179600-224181600	Active TSS	Fetal Intestine Large	intestine
39	chr1:224179600-224181600	Active TSS	A549	lung
40	chr1:224179600-224181600	Active TSS	HMEC	breast
41	chr1:224179600-224181600	Active TSS	HSMM	muscle
42	chr1:224179600-224181600	Active TSS	K562	blood
43	chr1:224179600-224181800	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr1:224179600-224181800	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr1:224179600-224181800	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr1:224179600-224181800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:224179600-224181800	Active TSS	Fetal Intestine Small	intestine
48	chr1:224179600-224181800	Active TSS	Stomach Smooth Muscle	stomach
49	chr1:224179600-224182200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:224179600-224182200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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