Variant report

Variant	rs60669636
Chromosome Location	chr1:159915424-159915425
allele	A/C
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	RCOR1	chr1:159915423-159915564	GM12878	blood:	n/a	n/a
2	E2F6	chr1:159915348-159915871	K562	blood:	n/a	chr1:159915640-159915652 chr1:159915554-159915565
3	POLR2A	chr1:159915268-159916156	MCF-7	breast:	n/a	n/a
4	SIX5	chr1:159915359-159915680	GM12878	blood:	n/a	chr1:159915539-159915553 chr1:159915540-159915549 chr1:159915542-159915551
5	NR2F2	chr1:159915396-159915952	K562	blood:	n/a	n/a
6	RAD21	chr1:159915071-159916406	SK-N-SH	brain:	n/a	chr1:159915585-159915604 chr1:159916095-159916105
7	ZBTB7A	chr1:159915052-159916277	ECC-1	luminal epithelium:	n/a	n/a
8	MYC	chr1:159915386-159916166	MCF10A-Er-Src	breast:	n/a	chr1:159915573-159915583 chr1:159915574-159915581
9	MYC	chr1:159915373-159915774	K562	blood:	n/a	chr1:159915573-159915583 chr1:159915574-159915581
10	RAD21	chr1:159915188-159916282	ECC-1	luminal epithelium:	n/a	chr1:159915585-159915604 chr1:159916095-159916105
11	TAF1	chr1:159915282-159916063	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr1:159915210-159916130	HCT-116	colon:	n/a	n/a
13	POLR2A	chr1:159915087-159916119	H1-hESC	embryonic stem cell:	n/a	n/a
14	YY1	chr1:159915330-159916091	HCT-116	colon:	n/a	n/a
15	NFYB	chr1:159915360-159915653	GM12878	blood:	n/a	n/a
16	CTCF	chr1:159915419-159915702	A549	lung:	n/a	chr1:159915582-159915603 chr1:159915587-159915605 chr1:159915590-159915600 chr1:159915588-159915604
17	SIX5	chr1:159915380-159915705	H1-hESC	embryonic stem cell:	n/a	chr1:159915539-159915553 chr1:159915540-159915549 chr1:159915542-159915551
18	GABPA	chr1:159915285-159915760	K562	blood:	n/a	n/a
19	MXI1	chr1:159913963-159916551	SK-N-SH	brain:	n/a	chr1:159915450-159915465 chr1:159915448-159915463
20	HA-E2F1	chr1:159915119-159916686	MCF-7	breast:	n/a	chr1:159915640-159915652
21	CTCF	chr1:159915195-159915800	K562	blood:	n/a	chr1:159915582-159915603 chr1:159915587-159915605 chr1:159915590-159915600 chr1:159915588-159915604
22	POLR2A	chr1:159914994-159916215	SK-N-MC	brain:	n/a	n/a
23	USF1	chr1:159915376-159915669	A549	lung:	n/a	n/a
24	POLR2A	chr1:159915386-159915939	MCF10A-Er-Src	breast:	n/a	n/a
25	MYC	chr1:159915313-159916085	MCF-7	breast:	n/a	chr1:159915573-159915583 chr1:159915350-159915360 chr1:159915574-159915581
26	CREB1	chr1:159915209-159915784	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr1:159915119-159916112	H1-hESC	embryonic stem cell:	n/a	n/a
28	SIX5	chr1:159915331-159915715	K562	blood:	n/a	chr1:159915539-159915553 chr1:159915540-159915549 chr1:159915542-159915551
29	SP4	chr1:159915264-159915721	H1-hESC	embryonic stem cell:	n/a	chr1:159915343-159915359 chr1:159915400-159915416
30	YY1	chr1:159915267-159916169	ECC-1	luminal epithelium:	n/a	n/a
31	ZBTB7A	chr1:159915290-159915822	K562	blood:	n/a	n/a
32	CTCF	chr1:159915410-159915761	IMR90	lung:	n/a	chr1:159915582-159915603 chr1:159915587-159915605 chr1:159915590-159915600 chr1:159915588-159915604
33	RCOR1	chr1:159915257-159915919	K562	blood:	n/a	n/a
34	ELF1	chr1:159915270-159915702	K562	blood:	n/a	n/a
35	ZBTB7A	chr1:159915037-159916151	ECC-1	luminal epithelium:	n/a	n/a
36	SP1	chr1:159915321-159915667	GM12878	blood:	n/a	chr1:159915404-159915416 chr1:159915515-159915527 chr1:159915420-159915429 chr1:159915404-159915416
37	TAF1	chr1:159915005-159916159	H1-hESC	embryonic stem cell:	n/a	n/a
38	GATA3	chr1:159915247-159916238	T-47D	breast:	n/a	chr1:159915283-159915294 chr1:159915463-159915476 chr1:159916047-159916054
39	POLR2A	chr1:159915153-159916235	H1-hESC	embryonic stem cell:	n/a	n/a
40	SIX5	chr1:159915317-159915749	K562	blood:	n/a	chr1:159915539-159915553 chr1:159915540-159915549 chr1:159915542-159915551
41	BACH1	chr1:159915153-159916113	H1-hESC	embryonic stem cell:	n/a	n/a
42	ETS1	chr1:159915375-159915696	K562	blood:	n/a	chr1:159915541-159915548 chr1:159915539-159915552
43	SIN3AK20	chr1:159915217-159916485	MCF-7	breast:	n/a	n/a
44	FOXP2	chr1:159915312-159915640	SK-N-MC	brain:	n/a	n/a
45	YY1	chr1:159915183-159915628	H1-hESC	embryonic stem cell:	n/a	n/a
46	IRF1	chr1:159915348-159915751	K562	blood:	n/a	chr1:159915409-159915423 chr1:159915404-159915418
47	USF1	chr1:159915382-159915715	A549	lung:	n/a	n/a
48	BHLHE40	chr1:159915368-159915956	K562	blood:	n/a	n/a
49	CREB1	chr1:159915422-159915631	A549	lung:	n/a	n/a
50	USF1	chr1:159915356-159915691	SK-N-SH_RA	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:159915374-159915424	AG04450	lung:	fetal
2	chr1:159915374-159915424	ovcar-3	ovarian:	n/a
3	chr1:159915374-159915424	HNPCEpiC	eye:	n/a
4	chr1:159915374-159915424	SAEC	small airway:	n/a
5	chr1:159915374-159915424	HepG2	liver:	n/a
6	chr1:159915374-159915424	GM12878	blood:	n/a
7	chr1:159915374-159915424	AG04449	skin:	fetal
8	chr1:159915374-159915424	ProgFib	skin:	n/a
9	chr1:159915374-159915424	PFSK-1	brain:	n/a
10	chr1:159915374-159915424	Hepatocyte	liver:	n/a
11	chr1:159915374-159915424	HRE	kidney:	n/a
12	chr1:159915374-159915424	Jurkat	blood:	n/a
13	chr1:159915374-159915424	MCF10A-Er-Src	breast:	n/a
14	chr1:159915374-159915424	HPAEpiC	pulmonary alveolar:	n/a
15	chr1:159915374-159915424	AG09309	skin:	n/a
16	chr1:159915374-159915424	RPTEC	kidney:	n/a
17	chr1:159915374-159915424	NB4	blood:	n/a
18	chr1:159915374-159915424	SK-N-MC	brain:	n/a
19	chr1:159915374-159915424	U87	brain:	n/a
20	chr1:159915374-159915424	A549	lung:	n/a
21	chr1:159915374-159915424	NH-A	brain:	n/a
22	chr1:159915374-159915424	NHDF-neo	bronchial:	n/a
23	chr1:159915374-159915424	MCF-7	breast:	n/a
24	chr1:159915374-159915424	HUVEC	blood vessel:	n/a
25	chr1:159915374-159915424	IMR90	lung:	fetal
26	chr1:159915374-159915424	NHBE	bronchial:	n/a
27	chr1:159915374-159915424	HIPEpiC	eye:	n/a
28	chr1:159915374-159915424	AoSMC	blood vessel:	n/a
29	chr1:159915374-159915424	Hela-S3	cervix:	n/a
30	chr1:159915374-159915424	LNCaP	prostate:	n/a
31	chr1:159915374-159915424	AG10803	skin:	n/a
32	chr1:159915374-159915424	PrEC	prostate:	n/a
33	chr1:159915374-159915424	K562	blood:	n/a
34	chr1:159915374-159915424	HMEC	breast:	n/a
35	chr1:159915374-159915424	SK-N-SH	brain:	n/a
36	chr1:159915374-159915424	HL-60	blood:	n/a
37	chr1:159915374-159915424	T-47D	breast:	n/a
38	chr1:159915374-159915424	SKMC	muscle:	n/a
39	chr1:159915374-159915424	CMK	blood:	n/a
40	chr1:159915374-159915424	HCT-116	colon:	n/a
41	chr1:159915374-159915424	ECC-1	luminal epithelium:	n/a
42	chr1:159915374-159915424	BJ	skin:	n/a
43	chr1:159915374-159915424	AG09319	gingival:	n/a
44	chr1:159915374-159915424	HCF	heart:	n/a
45	chr1:159915374-159915424	SK-N-SH_RA	brain:	n/a
46	chr1:159915374-159915424	HCM	heart:	n/a
47	chr1:159915374-159915424	NT2-D1	testis:	n/a
48	chr1:159915374-159915424	GM12891	blood:	n/a
49	chr1:159915374-159915424	HRPEpiC	eye:	n/a
50	chr1:159915374-159915424	HAEpiC	amniotic membrane:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:159914809..159917137-chr1:159930388..159932667,2	K562	blood:
2	chr1:159805798..159806345-chr1:159915418..159915964,2	K562	blood:
3	chr1:159893029..159897081-chr1:159913897..159916842,4	K562	blood:
4	chr1:159913973..159917644-chr1:159927852..159934070,11	MCF-7	breast:
5	chr1:159750451..159750989-chr1:159915127..159916035,2	K562	blood:
6	chr1:159914014..159917930-chr1:160000159..160002948,5	MCF-7	breast:

Variant related genes	Relation type
IGSF9	TF binding region
IGSF9	CpG island
ENSG00000158716	Chromatin interaction
ENSG00000224259	Chromatin interaction
ENSG00000158710	Chromatin interaction
ENSG00000143315	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2249707	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2789419	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2840582	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2840584	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2840585	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872489	chr1:159844819-159940000	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv524006	chr1:159886422-159923111	Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159913800-159915600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
2	chr1:159913800-159916200	Flanking Active TSS	HMEC	breast
3	chr1:159914000-159916200	Flanking Active TSS	Liver	Liver
4	chr1:159914200-159915800	Active TSS	Fetal Intestine Large	intestine
5	chr1:159914400-159916000	Active TSS	Fetal Intestine Small	intestine
6	chr1:159914400-159916200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr1:159914600-159915600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:159914600-159916000	Active TSS	H1 Cell Line	embryonic stem cell
9	chr1:159914600-159916000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:159914600-159916000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:159914600-159916000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:159914600-159916200	Active TSS	H9 Cell Line	embryonic stem cell
13	chr1:159914600-159916200	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr1:159914800-159915600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:159914800-159915600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:159914800-159915600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
17	chr1:159914800-159915800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:159914800-159915800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:159914800-159915800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:159914800-159916000	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr1:159914800-159916000	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr1:159914800-159916000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:159914800-159916000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
24	chr1:159914800-159916200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr1:159914800-159916200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:159914800-159916200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:159915000-159915600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
28	chr1:159915000-159915600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
29	chr1:159915000-159915600	Active TSS	Colonic Mucosa	Colon
30	chr1:159915000-159915800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
31	chr1:159915000-159915800	Active TSS	Placenta Amnion	Placenta Amnion
32	chr1:159915000-159915800	Bivalent/Poised TSS	NHLF	lung
33	chr1:159915000-159916000	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr1:159915000-159916000	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr1:159915000-159916000	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr1:159915000-159916000	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr1:159915000-159916000	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr1:159915000-159916000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr1:159915000-159916000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:159915000-159916000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:159915000-159916000	Active TSS	Brain Germinal Matrix	brain
42	chr1:159915000-159916000	Active TSS	Ovary	ovary
43	chr1:159915000-159916000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
44	chr1:159915000-159916000	Active TSS	NHEK	skin
45	chr1:159915000-159916200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:159915000-159916200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
47	chr1:159915000-159916400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:159915200-159915600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
49	chr1:159915200-159915600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:159915200-159915600	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood

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