Variant report

Variant	rs72991409
Chromosome Location	chr1:119930702-119930703
allele	C/T
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	USF1	chr1:119930368-119930761	H1-hESC	embryonic stem cell:	n/a	chr1:119930531-119930542
2	ZNF143	chr1:119930566-119930878	H1-hESC	embryonic stem cell:	n/a	n/a
3	TEAD4	chr1:119930351-119930783	H1-hESC	embryonic stem cell:	n/a	n/a
4	MYC	chr1:119930492-119930716	H1-hESC	embryonic stem cell:	n/a	chr1:119930527-119930546 chr1:119930531-119930542 chr1:119930617-119930627 chr1:119930532-119930541
5	TEAD4	chr1:119930400-119930750	H1-hESC	embryonic stem cell:	n/a	n/a
6	USF2	chr1:119930470-119930800	H1-hESC	embryonic stem cell:	n/a	n/a
7	MXI1	chr1:119930448-119930907	H1-hESC	embryonic stem cell:	n/a	chr1:119930617-119930626
8	MAX	chr1:119930450-119930880	H1-hESC	embryonic stem cell:	n/a	chr1:119930527-119930546 chr1:119930531-119930542 chr1:119930617-119930627 chr1:119930532-119930541
9	USF1	chr1:119930312-119930839	H1-hESC	embryonic stem cell:	n/a	chr1:119930531-119930542
10	MAX	chr1:119930445-119930825	H1-hESC	embryonic stem cell:	n/a	chr1:119930527-119930546 chr1:119930531-119930542 chr1:119930617-119930627 chr1:119930532-119930541
11	MAX	chr1:119930417-119930825	H1-hESC	embryonic stem cell:	n/a	chr1:119930527-119930546 chr1:119930531-119930542 chr1:119930617-119930627 chr1:119930532-119930541

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:119930673-119930723	H1-hESC	embryonic stem cell:	embryo
2	chr1:119930673-119930723	T-47D	breast:	n/a
3	chr1:119930673-119930723	Jurkat	blood:	n/a
4	chr1:119930673-119930723	RPTEC	kidney:	n/a
5	chr1:119930673-119930723	HMEC	breast:	n/a
6	chr1:119930673-119930723	PANC-1	pancreas:	n/a
7	chr1:119930673-119930723	NB4	blood:	n/a
8	chr1:119930673-119930723	HRCEpiC	kidney:	n/a
9	chr1:119930673-119930723	AG09309	skin:	n/a
10	chr1:119930673-119930723	AG10803	skin:	n/a
11	chr1:119930673-119930723	CMK	blood:	n/a
12	chr1:119930673-119930723	PrEC	prostate:	n/a
13	chr1:119930673-119930723	HRPEpiC	eye:	n/a
14	chr1:119930673-119930723	AoSMC	blood vessel:	n/a
15	chr1:119930673-119930723	HAEpiC	amniotic membrane:	n/a
16	chr1:119930673-119930723	HCM	heart:	n/a
17	chr1:119930673-119930723	MCF-7	breast:	n/a
18	chr1:119930673-119930723	NH-A	brain:	n/a
19	chr1:119930673-119930723	HCT-116	colon:	n/a
20	chr1:119930673-119930723	HL-60	blood:	n/a
21	chr1:119930673-119930723	ProgFib	skin:	n/a
22	chr1:119930673-119930723	HEK293	kidney:	embryo
23	chr1:119930673-119930723	SAEC	small airway:	n/a
24	chr1:119930673-119930723	K562	blood:	n/a
25	chr1:119930673-119930723	U87	brain:	n/a
26	chr1:119930673-119930723	HPAEpiC	pulmonary alveolar:	n/a
27	chr1:119930673-119930723	SK-N-SH	brain:	n/a
28	chr1:119930673-119930723	HNPCEpiC	eye:	n/a
29	chr1:119930673-119930723	HCPEpiC	choroid plexus:	n/a
30	chr1:119930673-119930723	Hepatocyte	liver:	n/a
31	chr1:119930673-119930723	AG04449	skin:	fetal
32	chr1:119930673-119930723	HEEpiC	esophagus:	n/a
33	chr1:119930673-119930723	IMR90	lung:	fetal
34	chr1:119930673-119930723	Caco-2	colon:	n/a
35	chr1:119930673-119930723	GM12891	blood:	n/a
36	chr1:119930673-119930723	SK-N-MC	brain:	n/a
37	chr1:119930673-119930723	ovcar-3	ovarian:	n/a
38	chr1:119930673-119930723	GM19239	blood:	n/a
39	chr1:119930673-119930723	SK-N-SH_RA	brain:	n/a
40	chr1:119930673-119930723	GM06990	blood:	n/a
41	chr1:119930673-119930723	HUVEC	blood vessel:	n/a
42	chr1:119930673-119930723	HIPEpiC	eye:	n/a
43	chr1:119930673-119930723	AG09319	gingival:	n/a
44	chr1:119930673-119930723	BJ	skin:	n/a
45	chr1:119930673-119930723	NHDF-neo	bronchial:	n/a
46	chr1:119930673-119930723	MCF10A-Er-Src	breast:	n/a
47	chr1:119930673-119930723	GM12892	blood:	n/a
48	chr1:119930673-119930723	NHBE	bronchial:	n/a
49	chr1:119930673-119930723	AG04450	lung:	fetal
50	chr1:119930673-119930723	HepG2	liver:	n/a

Variant related genes	Relation type
HAO2	TF binding region
HAO2	CpG island

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs34638261	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58135261	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58516954	0.93[AFR][1000 genomes]
rs59885709	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60055214	0.82[AFR][1000 genomes]
rs60069426	0.82[AFR][1000 genomes]
rs61275924	0.82[AFR][1000 genomes]
rs6663287	0.90[AMR][1000 genomes]
rs6704362	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs67248574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72563181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72989689	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72989690	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72989691	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72991408	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72991410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72991418	0.87[AFR][1000 genomes]
rs72991422	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7547008	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv917091	chr1:119688975-120023222	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv34089	chr1:119752112-120072961	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv1004662	chr1:119847447-120154798	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	esv2763647	chr1:119929442-120154798	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:119929600-119930800	Genic enhancers	Liver	Liver
2	chr1:119930400-119930800	Enhancers	Fetal Heart	heart
3	chr1:119930400-119931000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:119930400-119931200	Enhancers	H9 Cell Line	embryonic stem cell
5	chr1:119930400-119931200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr1:119930400-119931200	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr1:119930400-119931200	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr1:119930400-119931400	Enhancers	H1 Cell Line	embryonic stem cell
9	chr1:119930400-119931400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr1:119930600-119930800	Enhancers	Pancreas	Pancrea
11	chr1:119930600-119931000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr1:119930600-119931000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:119930600-119931200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:119930600-119931200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:119930600-119931200	Enhancers	HUES6 Cell Line	embryonic stem cell

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