Variant report

Variant	rs59279645
Chromosome Location	chr1:225150369-225150370
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr1:225150096-225150468	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:225150341-225150391	AG09309	skin:	n/a
2	chr1:225150341-225150391	BE2_C	brain:	n/a
3	chr1:225150341-225150391	HAEpiC	amniotic membrane:	n/a
4	chr1:225150341-225150391	HRCEpiC	kidney:	n/a
5	chr1:225150341-225150391	SK-N-MC	brain:	n/a
6	chr1:225150341-225150391	NHDF-neo	bronchial:	n/a
7	chr1:225150341-225150391	LNCaP	prostate:	n/a
8	chr1:225150341-225150391	HCM	heart:	n/a
9	chr1:225150341-225150391	SAEC	small airway:	n/a
10	chr1:225150341-225150391	AG10803	skin:	n/a
11	chr1:225150341-225150391	HEEpiC	esophagus:	n/a
12	chr1:225150341-225150391	U87	brain:	n/a
13	chr1:225150341-225150391	NH-A	brain:	n/a
14	chr1:225150341-225150391	SKMC	muscle:	n/a
15	chr1:225150341-225150391	Hela-S3	cervix:	n/a
16	chr1:225150341-225150391	IMR90	lung:	fetal
17	chr1:225150341-225150391	T-47D	breast:	n/a
18	chr1:225150341-225150391	ECC-1	luminal epithelium:	n/a
19	chr1:225150341-225150391	Jurkat	blood:	n/a
20	chr1:225150341-225150391	NHBE	bronchial:	n/a
21	chr1:225150341-225150391	HCF	heart:	n/a
22	chr1:225150341-225150391	H1-hESC	embryonic stem cell:	embryo
23	chr1:225150341-225150391	SK-N-SH	brain:	n/a
24	chr1:225150341-225150391	NB4	blood:	n/a
25	chr1:225150341-225150391	GM19239	blood:	n/a
26	chr1:225150341-225150391	HPAEpiC	pulmonary alveolar:	n/a
27	chr1:225150341-225150391	HepG2	liver:	n/a
28	chr1:225150341-225150391	HCT-116	colon:	n/a
29	chr1:225150341-225150391	PANC-1	pancreas:	n/a
30	chr1:225150341-225150391	ProgFib	skin:	n/a
31	chr1:225150341-225150391	AG04450	lung:	fetal
32	chr1:225150341-225150391	AG04449	skin:	fetal
33	chr1:225150341-225150391	SK-N-SH_RA	brain:	n/a
34	chr1:225150341-225150391	HL-60	blood:	n/a
35	chr1:225150341-225150391	HMEC	breast:	n/a
36	chr1:225150341-225150391	GM12891	blood:	n/a
37	chr1:225150341-225150391	HCPEpiC	choroid plexus:	n/a
38	chr1:225150341-225150391	CMK	blood:	n/a
39	chr1:225150341-225150391	BJ	skin:	n/a
40	chr1:225150341-225150391	PFSK-1	brain:	n/a
41	chr1:225150341-225150391	MCF10A-Er-Src	breast:	n/a
42	chr1:225150341-225150391	AG09319	gingival:	n/a
43	chr1:225150341-225150391	HRE	kidney:	n/a
44	chr1:225150341-225150391	PrEC	prostate:	n/a
45	chr1:225150341-225150391	HEK293	kidney:	embryo
46	chr1:225150341-225150391	NT2-D1	testis:	n/a
47	chr1:225150341-225150391	GM12892	blood:	n/a
48	chr1:225150341-225150391	HUVEC	blood vessel:	n/a
49	chr1:225150341-225150391	Caco-2	colon:	n/a
50	chr1:225150341-225150391	Hepatocyte	liver:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225146634..225148217-chr1:225149675..225151960,2	K562	blood:
2	chr1:225148681..225151534-chr1:225153143..225154709,2	K562	blood:

No data

Variant related genes	Relation type
DNAH14	TF binding region
DNAH14	CpG island

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10915712	1.00[EUR][1000 genomes]
rs10915713	1.00[EUR][1000 genomes]
rs58883363	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59263273	1.00[EUR][1000 genomes]
rs59777302	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59930091	0.94[AFR][1000 genomes]
rs60002937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60489231	1.00[EUR][1000 genomes]
rs60846144	1.00[EUR][1000 genomes]
rs61564365	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61732752	0.91[AFR][1000 genomes]
rs61745064	1.00[EUR][1000 genomes]
rs73127901	1.00[EUR][1000 genomes]
rs73129810	1.00[EUR][1000 genomes]
rs73129812	1.00[EUR][1000 genomes]
rs73129837	1.00[EUR][1000 genomes]
rs73129838	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73129850	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73129853	1.00[EUR][1000 genomes]
rs73129855	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73129861	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73129867	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73129870	1.00[EUR][1000 genomes]
rs73129894	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73129898	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73129900	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73131704	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73133542	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73133544	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73133554	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73133577	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73133578	1.00[EUR][1000 genomes]
rs73133591	1.00[EUR][1000 genomes]
rs73133599	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73133601	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73135010	1.00[EUR][1000 genomes]
rs7415021	0.91[AFR][1000 genomes]
rs7522229	1.00[EUR][1000 genomes]
rs7554589	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9659564	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757773	chr1:225087924-225253274	Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv2759001	chr1:225087924-225253274	Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1005824	chr1:225114654-225158871	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv3438976	chr1:225133567-225248753	Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv1804634	chr1:225137134-225206826	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225133600-225156200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:225138200-225152800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:225138600-225155600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:225138800-225163800	Weak transcription	Hela-S3	cervix
5	chr1:225140000-225158400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:225141400-225158800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:225141400-225162600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:225141600-225159000	Weak transcription	Ovary	ovary
9	chr1:225141800-225159400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:225141800-225160200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:225142800-225158400	Weak transcription	NH-A	brain
12	chr1:225142800-225162200	Weak transcription	Fetal Kidney	kidney
13	chr1:225142800-225164400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:225143400-225151800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:225143400-225161800	Weak transcription	A549	lung
16	chr1:225145200-225160600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:225145600-225152200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:225145600-225158800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:225147000-225157200	Strong transcription	K562	blood
20	chr1:225147400-225157800	Weak transcription	HepG2	liver
21	chr1:225148200-225156000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:225148400-225154400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:225148400-225158200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:225148600-225150400	Strong transcription	Primary hematopoietic stem cells	blood
25	chr1:225148600-225150400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:225148600-225150400	Strong transcription	Fetal Intestine Large	intestine
27	chr1:225148800-225158000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr1:225149400-225153000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:225149600-225151800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:225149800-225151600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:225150000-225150400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:225150000-225150400	ZNF genes & repeats	Fetal Intestine Small	intestine
33	chr1:225150000-225156000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:225150200-225150400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:225150200-225150400	ZNF genes & repeats	Liver	Liver
36	chr1:225150200-225150400	ZNF genes & repeats	Pancreas	Pancrea
37	chr1:225150200-225150800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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