Variant report

Variant	rs143993690
Chromosome Location	chr1:10489999-10490000
allele	-/ACTAT
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	CTCF	chr1:10489940-10490090	HVMF	connective:	n/a	n/a
2	MAX	chr1:10489978-10491108	HUVEC	blood vessel:	n/a	chr1:10490255-10490262
3	MAZ	chr1:10489707-10491577	IMR90	lung:	n/a	chr1:10490255-10490262
4	SMC3	chr1:10489751-10491449	SK-N-SH	brain:	n/a	chr1:10490428-10490438 chr1:10490424-10490438
5	HA-E2F1	chr1:10489950-10491592	MCF-7	breast:	n/a	chr1:10490750-10490759 chr1:10490696-10490706 chr1:10490431-10490440
6	CREB1	chr1:10489834-10491148	GM12878	blood:	n/a	n/a
7	PML	chr1:10489957-10491391	GM12878	blood:	n/a	n/a
8	MXI1	chr1:10489861-10491608	IMR90	lung:	n/a	chr1:10490791-10490806
9	POLR2A	chr1:10489904-10491135	HUVEC	blood vessel:	n/a	n/a
10	GATA2	chr1:10489832-10490480	HUVEC	blood vessel:	n/a	n/a
11	REST	chr1:10489888-10491538	H1-neurons	neurons:	n/a	chr1:10490770-10490783 chr1:10490697-10490707
12	MTA3	chr1:10489921-10491265	GM12878	blood:	n/a	n/a
13	MXI1	chr1:10489950-10491658	SK-N-SH	brain:	n/a	chr1:10490791-10490806
14	RAD21	chr1:10489837-10491455	SK-N-SH	brain:	n/a	chr1:10490428-10490438 chr1:10490378-10490388 chr1:10490696-10490709 chr1:10490423-10490442
15	SMC3	chr1:10489966-10491022	GM12878	blood:	n/a	chr1:10490428-10490438 chr1:10490424-10490438
16	RUNX3	chr1:10489882-10490698	GM12878	blood:	n/a	n/a
17	SPI1	chr1:10489944-10490129	K562	blood:	n/a	chr1:10490028-10490037
18	MBD4	chr1:10489996-10490545	HepG2	liver:	n/a	n/a
19	JUN	chr1:10489840-10491572	K562	blood:	n/a	n/a
20	E2F6	chr1:10489951-10491580	K562	blood:	n/a	chr1:10490750-10490759 chr1:10490696-10490706 chr1:10490431-10490440 chr1:10490495-10490506
21	CTCF	chr1:10489677-10491432	SK-N-SH	brain:	n/a	chr1:10490427-10490437 chr1:10490422-10490440 chr1:10490425-10490438 chr1:10490423-10490439 chr1:10490696-10490709 chr1:10490425-10490438 chr1:10490425-10490434
22	MYC	chr1:10489996-10490064	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr1:10489967-10491295	K562	blood:	n/a	n/a
24	POLR2A	chr1:10489889-10491699	H1-hESC	embryonic stem cell:	n/a	n/a
25	SPI1	chr1:10489908-10490092	GM12891	blood:	n/a	chr1:10490028-10490037
26	POLR2A	chr1:10489942-10491143	H1-hESC	embryonic stem cell:	n/a	n/a
27	FOS	chr1:10489853-10490616	HUVEC	blood vessel:	n/a	n/a
28	MAX	chr1:10489930-10491419	HCT-116	colon:	n/a	chr1:10490255-10490262
29	MAX	chr1:10489961-10491560	A549	lung:	n/a	chr1:10490255-10490262
30	E2F6	chr1:10489997-10491686	H1-hESC	embryonic stem cell:	n/a	chr1:10490750-10490759 chr1:10490696-10490706 chr1:10490431-10490440 chr1:10490495-10490506
31	POLR2A	chr1:10489842-10491400	SK-N-MC	brain:	n/a	n/a
32	E2F4	chr1:10489944-10491491	MCF10A-Er-Src	breast:	n/a	chr1:10490750-10490759 chr1:10490696-10490706 chr1:10490431-10490440 chr1:10490495-10490506
33	HEY1	chr1:10489949-10491133	K562	blood:	n/a	n/a
34	POLR2A	chr1:10489943-10491193	Raji	blood:	n/a	n/a
35	POLR2A	chr1:10489958-10491180	GM12892	blood:	n/a	n/a
36	POLR2A	chr1:10489992-10491033	GM12892	blood:	n/a	n/a
37	POLR2A	chr1:10489995-10490183	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr1:10489945-10491309	GM12892	blood:	n/a	n/a
39	POLR2A	chr1:10489770-10491307	HUVEC	blood vessel:	n/a	n/a
40	MAX	chr1:10489828-10491295	HCT-116	colon:	n/a	chr1:10490255-10490262
41	MAX	chr1:10489949-10491372	ECC-1	luminal epithelium:	n/a	chr1:10490255-10490262
42	MAX	chr1:10489957-10491499	ECC-1	luminal epithelium:	n/a	chr1:10490255-10490262
43	POLR2A	chr1:10489987-10491157	GM12878	blood:	n/a	n/a
44	CTCF	chr1:10489880-10490030	NHDF-neo	bronchial:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:10489962-10490012	GM06990	blood:	n/a
2	chr1:10489962-10490012	HEEpiC	esophagus:	n/a
3	chr1:10489962-10490012	BE2_C	brain:	n/a
4	chr1:10489962-10490012	T-47D	breast:	n/a
5	chr1:10489962-10490012	SKMC	muscle:	n/a
6	chr1:10489962-10490012	AG10803	skin:	n/a
7	chr1:10489962-10490012	NB4	blood:	n/a
8	chr1:10489962-10490012	AG04450	lung:	fetal
9	chr1:10489962-10490012	HL-60	blood:	n/a
10	chr1:10489962-10490012	HCPEpiC	choroid plexus:	n/a
11	chr1:10489962-10490012	HRPEpiC	eye:	n/a
12	chr1:10489962-10490012	HRE	kidney:	n/a
13	chr1:10489962-10490012	NHDF-neo	bronchial:	n/a
14	chr1:10489962-10490012	HAEpiC	amniotic membrane:	n/a
15	chr1:10489962-10490012	H1-hESC	embryonic stem cell:	embryo
16	chr1:10489962-10490012	MCF10A-Er-Src	breast:	n/a
17	chr1:10489962-10490012	RPTEC	kidney:	n/a
18	chr1:10489962-10490012	HNPCEpiC	eye:	n/a
19	chr1:10489962-10490012	NT2-D1	testis:	n/a
20	chr1:10489962-10490012	HUVEC	blood vessel:	n/a
21	chr1:10489962-10490012	Hela-S3	cervix:	n/a
22	chr1:10489962-10490012	K562	blood:	n/a
23	chr1:10489962-10490012	ECC-1	luminal epithelium:	n/a
24	chr1:10489962-10490012	HMEC	breast:	n/a
25	chr1:10489962-10490012	SK-N-SH	brain:	n/a
26	chr1:10489962-10490012	GM19239	blood:	n/a
27	chr1:10489962-10490012	AG09319	gingival:	n/a
28	chr1:10489962-10490012	IMR90	lung:	fetal
29	chr1:10489962-10490012	MCF-7	breast:	n/a
30	chr1:10489962-10490012	CMK	blood:	n/a
31	chr1:10489962-10490012	AoSMC	blood vessel:	n/a
32	chr1:10489962-10490012	U87	brain:	n/a
33	chr1:10489962-10490012	HPAEpiC	pulmonary alveolar:	n/a
34	chr1:10489962-10490012	SK-N-SH_RA	brain:	n/a
35	chr1:10489962-10490012	Hepatocyte	liver:	n/a
36	chr1:10489962-10490012	BJ	skin:	n/a
37	chr1:10489962-10490012	SAEC	small airway:	n/a
38	chr1:10489962-10490012	PFSK-1	brain:	n/a
39	chr1:10489962-10490012	AG04449	skin:	fetal
40	chr1:10489962-10490012	Jurkat	blood:	n/a
41	chr1:10489962-10490012	AG09309	skin:	n/a
42	chr1:10489962-10490012	GM12891	blood:	n/a
43	chr1:10489962-10490012	HCT-116	colon:	n/a
44	chr1:10489962-10490012	PrEC	prostate:	n/a
45	chr1:10489962-10490012	SK-N-MC	brain:	n/a
46	chr1:10489962-10490012	NHBE	bronchial:	n/a
47	chr1:10489962-10490012	ovcar-3	ovarian:	n/a
48	chr1:10489962-10490012	PANC-1	pancreas:	n/a
49	chr1:10489962-10490012	A549	lung:	n/a
50	chr1:10489962-10490012	NH-A	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:10475041..10475642-chr1:10489986..10490702,2	K562	blood:
2	chr1:10457794..10460664-chr1:10487844..10492697,5	K562	blood:
3	chr1:10488008..10492443-chr1:10531123..10534892,8	K562	blood:
4	chr1:10488905..10491611-chr1:10518532..10520834,2	MCF-7	breast:
5	chr1:10489993..10493018-chr1:10531254..10535234,5	MCF-7	breast:
6	chr1:10489448..10493967-chr1:10494423..10498103,7	K562	blood:
7	chr1:10457794..10461321-chr1:10487053..10491931,7	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DFFA-1	chr1:10489938-10490734	ENSG00000271989.1

Variant related genes	Relation type
APITD1	TF binding region
APITD1-CORT	TF binding region
APITD1-CORT	CpG island
APITD1	CpG island
ENSG00000251503	Chromatin interaction
ENSG00000142655	Chromatin interaction
ENSG00000142657	Chromatin interaction
ENSG00000160049	Chromatin interaction
ENSG00000203469	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	esv3373675	chr1:10489565-10491863	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10460000-10490200	Weak transcription	Psoas Muscle	Psoas
2	chr1:10461200-10490000	Weak transcription	Right Atrium	heart
3	chr1:10472000-10490000	Weak transcription	Stomach Mucosa	stomach
4	chr1:10475800-10490000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:10477800-10490000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:10477800-10490000	Weak transcription	Fetal Heart	heart
7	chr1:10478200-10490000	Weak transcription	Fetal Brain Male	brain
8	chr1:10479800-10490200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:10480200-10490000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:10480200-10490000	Weak transcription	Pancreas	Pancrea
11	chr1:10480200-10490400	Weak transcription	Aorta	Aorta
12	chr1:10480400-10490000	Weak transcription	Colonic Mucosa	Colon
13	chr1:10480400-10490000	Weak transcription	Small Intestine	intestine
14	chr1:10480400-10490000	Weak transcription	NH-A	brain
15	chr1:10480800-10490000	Weak transcription	Placenta	Placenta
16	chr1:10480800-10490200	Weak transcription	Left Ventricle	heart
17	chr1:10481000-10490000	Weak transcription	Right Ventricle	heart
18	chr1:10481200-10490000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:10481400-10490200	Weak transcription	Ovary	ovary
20	chr1:10481600-10490000	Weak transcription	Gastric	stomach
21	chr1:10481600-10490000	Weak transcription	HSMM	muscle
22	chr1:10481800-10490000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:10481800-10490000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:10481800-10490000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:10481800-10490000	Weak transcription	HSMMtube	muscle
26	chr1:10482000-10490000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:10482000-10490000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:10482000-10490000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:10482000-10490000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:10482000-10490000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:10482000-10490000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:10482000-10490000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr1:10482000-10490000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:10482000-10490000	Weak transcription	Esophagus	oesophagus
35	chr1:10482000-10490000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:10482000-10490000	Weak transcription	Spleen	Spleen
37	chr1:10482000-10490200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:10482200-10490000	Weak transcription	Thymus	Thymus
39	chr1:10482800-10490000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:10483400-10490000	Weak transcription	Fetal Brain Female	brain
41	chr1:10484600-10490000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:10484600-10490000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:10484600-10490000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:10484600-10490000	Weak transcription	Fetal Stomach	stomach
45	chr1:10484600-10490000	Weak transcription	NHLF	lung
46	chr1:10484800-10490000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:10484800-10490000	Weak transcription	Fetal Lung	lung
48	chr1:10484800-10490000	Weak transcription	NHDF-Ad	bronchial
49	chr1:10485000-10490000	Weak transcription	Liver	Liver
50	chr1:10487600-10490000	Enhancers	Duodenum Mucosa	Duodenum

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