Variant report

Variant	rs61091413
Chromosome Location	chr1:228136164-228136165
allele	C/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	HA-E2F1	chr1:228134238-228136316	MCF-7	breast:	n/a	chr1:228136050-228136059
2	NRF1	chr1:228136156-228136307	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTBP2	chr1:228135569-228136528	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr1:228136040-228136190	SK-N-SH_RA	brain:	n/a	n/a
5	BRCA1	chr1:228136160-228136311	Hela-S3	cervix:	n/a	n/a
6	SIN3A	chr1:228135507-228136571	H1-hESC	embryonic stem cell:	n/a	n/a
7	TCF12	chr1:228133787-228136169	ECC-1	luminal epithelium:	n/a	chr1:228134156-228134166 chr1:228134108-228134115
8	ZBTB7A	chr1:228135687-228136429	ECC-1	luminal epithelium:	n/a	chr1:228135964-228135973
9	HMGN3	chr1:228133998-228136236	K562	blood:	n/a	chr1:228134130-228134139 chr1:228134127-228134136
10	HA-E2F1	chr1:228135170-228136222	Hela-S3	cervix:	n/a	chr1:228136050-228136059
11	ZBTB7A	chr1:228135308-228136203	K562	blood:	n/a	chr1:228135964-228135973
12	SMARCB1	chr1:228135104-228136347	Hela-S3	cervix:	n/a	n/a
13	TFAP2C	chr1:228135505-228136530	Hela-S3	cervix:	n/a	n/a
14	ZBTB7A	chr1:228135564-228136326	ECC-1	luminal epithelium:	n/a	chr1:228135964-228135973
15	UBTF	chr1:228133969-228136371	K562	blood:	n/a	n/a
16	MAZ	chr1:228135201-228136357	Hela-S3	cervix:	n/a	chr1:228135877-228135887
17	TFAP2A	chr1:228135431-228136358	Hela-S3	cervix:	n/a	chr1:228135992-228136004 chr1:228135992-228136004 chr1:228135992-228136004 chr1:228135995-228136003 chr1:228135995-228136003 chr1:228135992-228136004 chr1:228135995-228136003
18	SIN3AK20	chr1:228135047-228136318	PANC-1	pancreas:	n/a	n/a
19	MAX	chr1:228133768-228136454	A549	lung:	n/a	chr1:228135877-228135887 chr1:228134844-228134855 chr1:228134529-228134540
20	MAZ	chr1:228135509-228136278	K562	blood:	n/a	chr1:228135877-228135887
21	UBTF	chr1:228136146-228136203	K562	blood:	n/a	n/a
22	ZNF263	chr1:228136096-228136513	HEK293-T-REx	kidney:	n/a	n/a
23	MAZ	chr1:228134820-228136540	IMR90	lung:	n/a	chr1:228135877-228135887 chr1:228134844-228134855

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:228136127-228136177	AG09309	skin:	n/a
2	chr1:228136127-228136177	SK-N-MC	brain:	n/a
3	chr1:228136127-228136177	ovcar-3	ovarian:	n/a
4	chr1:228136127-228136177	HRCEpiC	kidney:	n/a
5	chr1:228136127-228136177	GM12878	blood:	n/a
6	chr1:228136127-228136177	PANC-1	pancreas:	n/a
7	chr1:228136127-228136177	NHBE	bronchial:	n/a
8	chr1:228136127-228136177	HepG2	liver:	n/a
9	chr1:228136127-228136177	ProgFib	skin:	n/a
10	chr1:228136127-228136177	HEK293	kidney:	embryo
11	chr1:228136127-228136177	HNPCEpiC	eye:	n/a
12	chr1:228136127-228136177	HRPEpiC	eye:	n/a
13	chr1:228136127-228136177	GM19239	blood:	n/a
14	chr1:228136127-228136177	HIPEpiC	eye:	n/a
15	chr1:228136127-228136177	GM06990	blood:	n/a
16	chr1:228136127-228136177	HL-60	blood:	n/a
17	chr1:228136127-228136177	AG04449	skin:	fetal
18	chr1:228136127-228136177	LNCaP	prostate:	n/a
19	chr1:228136127-228136177	K562	blood:	n/a
20	chr1:228136127-228136177	H1-hESC	embryonic stem cell:	embryo
21	chr1:228136127-228136177	ECC-1	luminal epithelium:	n/a
22	chr1:228136127-228136177	HCM	heart:	n/a
23	chr1:228136127-228136177	Caco-2	colon:	n/a
24	chr1:228136127-228136177	AG04450	lung:	fetal
25	chr1:228136127-228136177	HUVEC	blood vessel:	n/a
26	chr1:228136127-228136177	HCT-116	colon:	n/a
27	chr1:228136127-228136177	SK-N-SH	brain:	n/a
28	chr1:228136127-228136177	BJ	skin:	n/a
29	chr1:228136127-228136177	HPAEpiC	pulmonary alveolar:	n/a
30	chr1:228136127-228136177	HRE	kidney:	n/a
31	chr1:228136127-228136177	HCPEpiC	choroid plexus:	n/a
32	chr1:228136127-228136177	A549	lung:	n/a
33	chr1:228136127-228136177	AG09319	gingival:	n/a
34	chr1:228136127-228136177	BE2_C	brain:	n/a
35	chr1:228136127-228136177	AoSMC	blood vessel:	n/a
36	chr1:228136127-228136177	HCF	heart:	n/a
37	chr1:228136127-228136177	PFSK-1	brain:	n/a
38	chr1:228136127-228136177	Hela-S3	cervix:	n/a
39	chr1:228136127-228136177	HEEpiC	esophagus:	n/a
40	chr1:228136127-228136177	PrEC	prostate:	n/a
41	chr1:228136127-228136177	Jurkat	blood:	n/a
42	chr1:228136127-228136177	T-47D	breast:	n/a
43	chr1:228136127-228136177	HAEpiC	amniotic membrane:	n/a
44	chr1:228136127-228136177	CMK	blood:	n/a
45	chr1:228136127-228136177	NHDF-neo	bronchial:	n/a
46	chr1:228136127-228136177	GM12892	blood:	n/a
47	chr1:228136127-228136177	HMEC	breast:	n/a
48	chr1:228136127-228136177	NB4	blood:	n/a
49	chr1:228136127-228136177	MCF10A-Er-Src	breast:	n/a
50	chr1:228136127-228136177	RPTEC	kidney:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:227916221..227923035-chr1:228131852..228141791,18	MCF-7	breast:
2	chr1:228128193..228132003-chr1:228132864..228136285,5	K562	blood:
3	chr1:227962379..227965351-chr1:228135797..228137632,2	MCF-7	breast:

Variant related genes	Relation type
WNT9A	TF binding region
WNT9A	CpG island
ENSG00000081692	Chromatin interaction
ENSG00000264483	Chromatin interaction
ENSG00000143740	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs16848361	1.00[EUR][1000 genomes]
rs2231711	1.00[EUR][1000 genomes]
rs34658204	1.00[EUR][1000 genomes]
rs41270181	1.00[EUR][1000 genomes]
rs41314262	1.00[EUR][1000 genomes]
rs45460992	1.00[EUR][1000 genomes]
rs56280452	1.00[EUR][1000 genomes]
rs56394518	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57624754	1.00[EUR][1000 genomes]
rs58696607	1.00[EUR][1000 genomes]
rs58787263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60538700	1.00[EUR][1000 genomes]
rs60642596	1.00[EUR][1000 genomes]
rs60777646	1.00[EUR][1000 genomes]
rs73108778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74140818	1.00[EUR][1000 genomes]
rs74140819	1.00[EUR][1000 genomes]
rs74140821	1.00[EUR][1000 genomes]
rs74140822	1.00[EUR][1000 genomes]
rs74140823	1.00[EUR][1000 genomes]
rs74140994	1.00[EUR][1000 genomes]
rs74143607	1.00[EUR][1000 genomes]
rs74143612	1.00[EUR][1000 genomes]
rs74143614	1.00[EUR][1000 genomes]
rs74143615	1.00[EUR][1000 genomes]
rs74143616	1.00[EUR][1000 genomes]
rs8192631	1.00[EUR][1000 genomes]
rs9662484	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
7	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
9	nsv873251	chr1:228051234-228160911	Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	esv3344015	chr1:228134354-228137302	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	esv3428054	chr1:228134779-228136852	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription 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:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228133800-228136400	Active TSS	NHLF	lung
2	chr1:228134000-228136200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr1:228134000-228136400	Active TSS	Psoas Muscle	Psoas
4	chr1:228134200-228136200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:228134200-228136200	Enhancers	Liver	Liver
6	chr1:228134200-228136200	Active TSS	HSMM	muscle
7	chr1:228134200-228136400	Active TSS	Ovary	ovary
8	chr1:228134200-228136400	Active TSS	HSMMtube	muscle
9	chr1:228134200-228136800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr1:228134400-228136200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr1:228134400-228136200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:228134400-228136200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:228134400-228136200	Active TSS	Brain Anterior Caudate	brain
14	chr1:228134400-228136200	Active TSS	Colon Smooth Muscle	Colon
15	chr1:228134400-228136200	Active TSS	Esophagus	oesophagus
16	chr1:228134400-228136200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
17	chr1:228134400-228136200	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr1:228134400-228136200	Active TSS	Fetal Stomach	stomach
19	chr1:228134400-228136200	Active TSS	Gastric	stomach
20	chr1:228134400-228136200	Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr1:228134400-228136200	Active TSS	A549	lung
22	chr1:228134400-228136400	Active TSS	Left Ventricle	heart
23	chr1:228134400-228136400	Active TSS	Rectal Smooth Muscle	rectum
24	chr1:228134400-228136600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:228134400-228136800	Active TSS	Hela-S3	cervix
26	chr1:228134600-228136200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr1:228134600-228136200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
28	chr1:228134600-228136200	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr1:228134600-228136200	Active TSS	Aorta	Aorta
30	chr1:228134600-228136200	Bivalent/Poised TSS	Fetal Brain Female	brain
31	chr1:228134600-228136200	Active TSS	Lung	lung
32	chr1:228134600-228136200	Active TSS	NHDF-Ad	bronchial
33	chr1:228134600-228136400	Active TSS	Brain Angular Gyrus	brain
34	chr1:228134600-228136600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:228134600-228136600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:228134600-228136800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
37	chr1:228134800-228136200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:228134800-228136200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
39	chr1:228134800-228136200	Active TSS	Fetal Lung	lung
40	chr1:228134800-228136200	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr1:228134800-228136200	Active TSS	Stomach Smooth Muscle	stomach
42	chr1:228134800-228136400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:228134800-228136400	Active TSS	Right Atrium	heart
44	chr1:228135000-228136200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:228135000-228136200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:228135000-228136200	Active TSS	Muscle Satellite Cultured Cells	--
47	chr1:228135000-228136200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
48	chr1:228135000-228136200	Active TSS	HMEC	breast
49	chr1:228135000-228136400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
50	chr1:228135200-228136200	Active TSS	H1 Cell Line	embryonic stem cell

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