Variant report

Variant	rs543590208
Chromosome Location	chr1:180198788-180198789
allele	-/CGGAGCGCGCTCCGTCCGG
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	CTBP2	chr1:180197846-180199045	H1-hESC	embryonic stem cell:	n/a	n/a
2	HMGN3	chr1:180198110-180199328	K562	blood:	n/a	n/a
3	MAX	chr1:180198747-180199194	K562	blood:	n/a	n/a
4	TBL1XR1	chr1:180198781-180198792	K562	blood:	n/a	n/a
5	MAX	chr1:180198756-180199099	K562	blood:	n/a	n/a
6	MAX	chr1:180197913-180199255	ECC-1	luminal epithelium:	n/a	n/a
7	MYC	chr1:180198728-180198900	MCF-7	breast:	n/a	n/a
8	MAX	chr1:180198568-180199536	MCF-7	breast:	n/a	chr1:180199482-180199492
9	E2F6	chr1:180197561-180199243	H1-hESC	embryonic stem cell:	n/a	chr1:180199215-180199225 chr1:180198561-180198571 chr1:180199214-180199223
10	ZKSCAN1	chr1:180198751-180199041	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:180198472-180199267	MCF-7	breast:	n/a	n/a
12	EGR1	chr1:180198620-180199357	HCT-116	colon:	n/a	chr1:180199316-180199326
13	SIN3AK20	chr1:180198701-180198947	H1-hESC	embryonic stem cell:	n/a	n/a
14	E2F6	chr1:180198508-180199126	K562	blood:	n/a	chr1:180198561-180198571
15	UBTF	chr1:180198327-180199086	K562	blood:	n/a	n/a
16	MAX	chr1:180197799-180199538	ECC-1	luminal epithelium:	n/a	chr1:180199482-180199492
17	EGR1	chr1:180198566-180199117	H1-hESC	embryonic stem cell:	n/a	n/a
18	E2F6	chr1:180198626-180199227	A549	lung:	n/a	chr1:180199215-180199225 chr1:180199214-180199223
19	GTF2F1	chr1:180198592-180199042	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr1:180198121-180199141	HepG2	liver:	n/a	n/a
21	JUND	chr1:180198373-180198897	H1-hESC	embryonic stem cell:	n/a	n/a
22	E2F6	chr1:180197892-180199368	K562	blood:	n/a	chr1:180199215-180199225 chr1:180198561-180198571 chr1:180199214-180199223
23	GABPA	chr1:180198565-180198959	H1-hESC	embryonic stem cell:	n/a	n/a
24	MYC	chr1:180198627-180199753	NB4	blood:	n/a	chr1:180199482-180199492
25	TCF12	chr1:180198662-180199804	ECC-1	luminal epithelium:	n/a	n/a
26	ZBTB7A	chr1:180198135-180200333	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr1:180198712-180199210	ProgFib	skin:	n/a	n/a
28	ZNF143	chr1:180198691-180198891	H1-hESC	embryonic stem cell:	n/a	n/a
29	ZNF263	chr1:180198430-180199021	HEK293-T-REx	kidney:	n/a	chr1:180198755-180198764
30	CTCF	chr1:180198714-180198795	Pancreas_OC	pancreas:	n/a	n/a
31	SUZ12	chr1:180197213-180199016	NT2-D1	testis:	n/a	n/a
32	POLR2A	chr1:180198770-180199298	H1-hESC	embryonic stem cell:	n/a	n/a
33	SIN3A	chr1:180198105-180201535	H1-hESC	embryonic stem cell:	n/a	chr1:180199800-180199811 chr1:180201367-180201377 chr1:180200185-180200198 chr1:180198586-180198597 chr1:180198584-180198597
34	TBP	chr1:180198778-180199157	K562	blood:	n/a	n/a
35	HA-E2F1	chr1:180197498-180198973	MCF-7	breast:	n/a	chr1:180198561-180198571
36	ZBTB7A	chr1:180198413-180199116	K562	blood:	n/a	n/a
37	MAX	chr1:180198242-180198920	A549	lung:	n/a	n/a
38	MYC	chr1:180198741-180199051	K562	blood:	n/a	n/a
39	CTCF	chr1:180198680-180198830	SK-N-SH_RA	brain:	n/a	chr1:180198796-180198809
40	BACH1	chr1:180198468-180199024	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAX	chr1:180197655-180199566	H1-hESC	embryonic stem cell:	n/a	chr1:180199482-180199492
42	POLR2A	chr1:180198562-180199636	HEK293	kidney:	n/a	n/a
43	PAX5	chr1:180198755-180199077	GM12892	blood:	n/a	n/a
44	POLR2A	chr1:180198704-180199062	A549	lung:	n/a	n/a
45	E2F6	chr1:180197762-180199140	H1-hESC	embryonic stem cell:	n/a	chr1:180198561-180198571
46	POLR2A	chr1:180198684-180199242	PFSK-1	brain:	n/a	n/a
47	POLR2A	chr1:180198687-180199573	MCF-7	breast:	n/a	n/a
48	POLR2A	chr1:180198604-180199136	A549	lung:	n/a	n/a
49	MAX	chr1:180197976-180199478	K562	blood:	n/a	n/a
50	POLR2A	chr1:180198359-180199142	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:180197504..180199167-chr1:180224925..180226535,2	MCF-7	breast:
2	chr1:179832613..179834557-chr1:180196646..180198975,2	MCF-7	breast:
3	chr1:180197757..180200322-chr1:180217302..180220148,2	K562	blood:
4	chr1:180157764..180160729-chr1:180196773..180199044,2	MCF-7	breast:
5	chr1:180197528..180200245-chr1:180468948..180472883,3	MCF-7	breast:
6	chr1:180196398..180198939-chr20:52539225..52540761,2	MCF-7	breast:
7	chr1:180179631..180182619-chr1:180197309..180199073,2	K562	blood:

Variant related genes	Relation type
LHX4	TF binding region
ENSG00000121454	Chromatin interaction
ENSG00000258664	Chromatin interaction
ENSG00000135847	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv1012558	chr1:180027960-180217613	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv535218	chr1:180027960-180217613	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv497930	chr1:180031321-180220723	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv533073	chr1:180031328-180217612	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv916937	chr1:180031328-180220685	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv1007590	chr1:180121480-180236452	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv999104	chr1:180121480-180242659	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv1002133	chr1:180127036-180230081	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv1011134	chr1:180127616-180201104	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv999182	chr1:180127616-180236452	Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	nsv1005512	chr1:180127616-180242659	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv832004	chr1:180128502-180335540	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
16	nsv1012816	chr1:180132688-180201104	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
17	nsv1012145	chr1:180132688-180236452	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
18	nsv466239	chr1:180145978-180268476	Bivalent Enhancer ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
19	nsv548345	chr1:180145978-180268476	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
20	nsv1005793	chr1:180150400-180205202	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
21	nsv1005073	chr1:180152550-180250783	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
22	nsv535219	chr1:180152550-180250783	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
23	nsv1001477	chr1:180172903-180298287	Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
24	nsv535220	chr1:180172903-180298287	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
25	nsv498075	chr1:180179441-180278544	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS 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
26	nsv872575	chr1:180186713-180238243	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
27	esv3361812	chr1:180197754-180200702	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
28	esv14202	chr1:180198652-180200893	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180197400-180201000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:180197600-180201000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr1:180197800-180198800	Bivalent Enhancer	Fetal Brain Male	brain
4	chr1:180197800-180201000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr1:180197800-180201000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr1:180197800-180201000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:180197800-180201200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr1:180198000-180198800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
9	chr1:180198000-180198800	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
10	chr1:180198000-180199000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
11	chr1:180198000-180199000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
12	chr1:180198000-180199000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
13	chr1:180198000-180200600	Bivalent/Poised TSS	NHEK	skin
14	chr1:180198000-180201000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr1:180198200-180198800	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:180198200-180198800	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:180198200-180198800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
18	chr1:180198200-180198800	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:180198200-180198800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
20	chr1:180198200-180198800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
21	chr1:180198200-180198800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
22	chr1:180198200-180198800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
23	chr1:180198200-180198800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
24	chr1:180198200-180198800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
25	chr1:180198200-180198800	Flanking Active TSS	Gastric	stomach
26	chr1:180198200-180198800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
27	chr1:180198200-180199000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
28	chr1:180198200-180199000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:180198200-180199000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:180198200-180199000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:180198200-180199000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:180198200-180199000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:180198200-180199000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:180198200-180199000	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:180198200-180199000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
36	chr1:180198200-180199000	Flanking Bivalent TSS/Enh	Placenta Amnion	Placenta Amnion
37	chr1:180198200-180199000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
38	chr1:180198200-180199000	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
39	chr1:180198200-180199000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
40	chr1:180198200-180199000	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
41	chr1:180198200-180199200	Bivalent Enhancer	Fetal Intestine Large	intestine
42	chr1:180198200-180199600	Bivalent/Poised TSS	Fetal Brain Female	brain
43	chr1:180198200-180199600	Bivalent/Poised TSS	Osteobl	bone
44	chr1:180198200-180200000	Flanking Bivalent TSS/Enh	Thymus	Thymus
45	chr1:180198200-180201000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
46	chr1:180198400-180198800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:180198400-180198800	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:180198400-180198800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:180198400-180198800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:180198400-180198800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood

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