Variant report

Variant	rs12077115
Chromosome Location	chr1:225924711-225924712
allele	A/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	MYC	chr1:225924563-225925286	MCF10A-Er-Src	breast:	n/a	n/a
2	FOSL2	chr1:225924544-225925208	A549	lung:	n/a	n/a
3	FOS	chr1:225924441-225925309	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr1:225924558-225925194	MCF10A-Er-Src	breast:	n/a	n/a
5	GATA2	chr1:225923236-225925427	SH-SY5Y	brain:	n/a	chr1:225923678-225923685 chr1:225924034-225924041
6	TBP	chr1:225924426-225925375	Hela-S3	cervix:	n/a	n/a
7	MXI1	chr1:225924304-225925296	Hela-S3	cervix:	n/a	n/a
8	MAZ	chr1:225924015-225925557	Hela-S3	cervix:	n/a	n/a
9	TCF12	chr1:225924591-225925467	A549	lung:	n/a	n/a
10	RCOR1	chr1:225924290-225925696	Hela-S3	cervix:	n/a	n/a
11	CEBPB	chr1:225922960-225925434	Hela-S3	cervix:	n/a	chr1:225924703-225924714 chr1:225923420-225923433 chr1:225924702-225924715 chr1:225924702-225924715 chr1:225923420-225923431 chr1:225923246-225923258
12	MAX	chr1:225923149-225925666	Hela-S3	cervix:	n/a	n/a
13	PRDM1	chr1:225924640-225925304	Hela-S3	cervix:	n/a	chr1:225924880-225924889 chr1:225924875-225924890
14	MYC	chr1:225924245-225925240	Hela-S3	cervix:	n/a	n/a
15	MYC	chr1:225924489-225925206	MCF10A-Er-Src	breast:	n/a	n/a
16	BRCA1	chr1:225923201-225925446	Hela-S3	cervix:	n/a	n/a
17	RAD21	chr1:225924483-225925292	Hela-S3	cervix:	n/a	chr1:225925047-225925060 chr1:225925046-225925058 chr1:225925048-225925058
18	GTF2F1	chr1:225924296-225925358	Hela-S3	cervix:	n/a	n/a
19	MAX	chr1:225924249-225925804	Hela-S3	cervix:	n/a	n/a
20	NFIC	chr1:225923980-225925352	ECC-1	luminal epithelium:	n/a	chr1:225925113-225925129 chr1:225925112-225925129
21	FOS	chr1:225924426-225925286	MCF10A-Er-Src	breast:	n/a	n/a
22	RFX5	chr1:225923152-225925273	Hela-S3	cervix:	n/a	n/a
23	CEBPB	chr1:225924469-225925031	IMR90	lung:	n/a	chr1:225924703-225924714 chr1:225924702-225924715 chr1:225924702-225924715
24	CHD2	chr1:225924423-225925310	Hela-S3	cervix:	n/a	n/a
25	STAT3	chr1:225924414-225925258	Hela-S3	cervix:	n/a	chr1:225924931-225924939
26	CEBPB	chr1:225924313-225925235	A549	lung:	n/a	chr1:225924703-225924714 chr1:225924702-225924715 chr1:225924702-225924715
27	EP300	chr1:225924530-225925400	Hela-S3	cervix:	n/a	chr1:225924599-225924609 chr1:225924907-225924921
28	SMC3	chr1:225923090-225925575	Hela-S3	cervix:	n/a	n/a
29	MAFK	chr1:225924222-225925430	Hela-S3	cervix:	n/a	n/a
30	TCF7L2	chr1:225923022-225925297	Hela-S3	cervix:	n/a	chr1:225924315-225924324 chr1:225924311-225924327 chr1:225924313-225924323 chr1:225924311-225924327 chr1:225924312-225924326
31	SMARCC1	chr1:225923135-225925839	Hela-S3	cervix:	n/a	n/a
32	CEBPB	chr1:225924479-225924892	HepG2	liver:	n/a	chr1:225924703-225924714 chr1:225924702-225924715 chr1:225924702-225924715
33	STAT3	chr1:225924461-225925170	MCF10A-Er-Src	breast:	n/a	chr1:225924931-225924939
34	STAT3	chr1:225924404-225925227	MCF10A-Er-Src	breast:	n/a	chr1:225924931-225924939
35	ZKSCAN1	chr1:225924605-225925513	Hela-S3	cervix:	n/a	n/a
36	EP300	chr1:225924242-225924769	SK-N-SH_RA	brain:	n/a	chr1:225924599-225924609 chr1:225924362-225924378
37	STAT3	chr1:225924576-225925255	MCF10A-Er-Src	breast:	n/a	chr1:225924931-225924939
38	TFAP2C	chr1:225924202-225925551	Hela-S3	cervix:	n/a	n/a
39	USF2	chr1:225924555-225925403	Hela-S3	cervix:	n/a	n/a
40	CEBPB	chr1:225924473-225925338	A549	lung:	n/a	chr1:225924703-225924714 chr1:225924702-225924715 chr1:225924702-225924715
41	NFIC	chr1:225924110-225925488	ECC-1	luminal epithelium:	n/a	chr1:225925113-225925129 chr1:225925112-225925129
42	E2F4	chr1:225924419-225924990	MCF10A-Er-Src	breast:	n/a	n/a
43	TFAP2A	chr1:225924182-225925440	Hela-S3	cervix:	n/a	n/a
44	FOS	chr1:225924640-225925158	MCF10A-Er-Src	breast:	n/a	n/a
45	NFIC	chr1:225924137-225925477	SK-N-SH	brain:	n/a	chr1:225925113-225925129 chr1:225925112-225925129

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:225924665-225924715	SAEC	small airway:	n/a
2	chr1:225924665-225924715	U87	brain:	n/a
3	chr1:225924665-225924715	NH-A	brain:	n/a
4	chr1:225924665-225924715	K562	blood:	n/a
5	chr1:225924665-225924715	HPAEpiC	pulmonary alveolar:	n/a
6	chr1:225924665-225924715	GM06990	blood:	n/a
7	chr1:225924665-225924715	RPTEC	kidney:	n/a
8	chr1:225924665-225924715	HIPEpiC	eye:	n/a
9	chr1:225924665-225924715	GM12891	blood:	n/a
10	chr1:225924665-225924715	PFSK-1	brain:	n/a
11	chr1:225924665-225924715	MCF10A-Er-Src	breast:	n/a
12	chr1:225924665-225924715	HAEpiC	amniotic membrane:	n/a
13	chr1:225924665-225924715	NHBE	bronchial:	n/a
14	chr1:225924665-225924715	SK-N-SH_RA	brain:	n/a
15	chr1:225924665-225924715	Jurkat	blood:	n/a
16	chr1:225924665-225924715	HEK293	kidney:	embryo
17	chr1:225924665-225924715	HCF	heart:	n/a
18	chr1:225924665-225924715	AoSMC	blood vessel:	n/a
19	chr1:225924665-225924715	AG09309	skin:	n/a
20	chr1:225924665-225924715	SK-N-MC	brain:	n/a
21	chr1:225924665-225924715	H1-hESC	embryonic stem cell:	embryo
22	chr1:225924665-225924715	Hela-S3	cervix:	n/a
23	chr1:225924665-225924715	ovcar-3	ovarian:	n/a
24	chr1:225924665-225924715	NHDF-neo	bronchial:	n/a
25	chr1:225924665-225924715	BJ	skin:	n/a
26	chr1:225924665-225924715	SK-N-SH	brain:	n/a
27	chr1:225924665-225924715	BE2_C	brain:	n/a
28	chr1:225924665-225924715	HCM	heart:	n/a
29	chr1:225924665-225924715	NB4	blood:	n/a
30	chr1:225924665-225924715	Hepatocyte	liver:	n/a
31	chr1:225924665-225924715	HepG2	liver:	n/a
32	chr1:225924665-225924715	T-47D	breast:	n/a
33	chr1:225924665-225924715	AG10803	skin:	n/a
34	chr1:225924665-225924715	HRE	kidney:	n/a
35	chr1:225924665-225924715	AG09319	gingival:	n/a
36	chr1:225924665-225924715	HCPEpiC	choroid plexus:	n/a
37	chr1:225924665-225924715	HL-60	blood:	n/a
38	chr1:225924665-225924715	GM19239	blood:	n/a
39	chr1:225924665-225924715	GM12892	blood:	n/a
40	chr1:225924665-225924715	AG04450	lung:	fetal
41	chr1:225924665-225924715	HUVEC	blood vessel:	n/a
42	chr1:225924665-225924715	AG04449	skin:	fetal
43	chr1:225924665-225924715	HNPCEpiC	eye:	n/a
44	chr1:225924665-225924715	GM12878	blood:	n/a
45	chr1:225924665-225924715	LNCaP	prostate:	n/a
46	chr1:225924665-225924715	HRPEpiC	eye:	n/a
47	chr1:225924665-225924715	ECC-1	luminal epithelium:	n/a
48	chr1:225924665-225924715	CMK	blood:	n/a
49	chr1:225924665-225924715	IMR90	lung:	fetal
50	chr1:225924665-225924715	HRCEpiC	kidney:	n/a

Variant related genes	Relation type
RNU6-1304P	TF binding region
ENSG00000226349	TF binding region
RNU6-1304P	CpG island
ENSG00000226349	CpG island

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10915864	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10915865	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10915866	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10915868	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11588772	0.81[EUR][1000 genomes]
rs11589433	0.95[ASN][1000 genomes]
rs12076509	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12081218	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17570271	0.91[EUR][1000 genomes]
rs4653429	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4653655	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4653660	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4653662	0.95[ASN][1000 genomes]
rs7525768	0.85[AMR][1000 genomes];0.86[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	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv525391	chr1:225912620-225928538	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225915200-225933600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:225921400-225925600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:225921400-225934400	Weak transcription	Esophagus	oesophagus
4	chr1:225922200-225925800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:225922800-225925400	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr1:225922800-225925600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:225922800-225925800	Enhancers	Liver	Liver
8	chr1:225922800-225925800	Enhancers	Fetal Lung	lung
9	chr1:225922800-225926000	Enhancers	Fetal Muscle Leg	muscle
10	chr1:225923000-225924800	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr1:225923000-225925000	Enhancers	Fetal Stomach	stomach
12	chr1:225923000-225925200	Enhancers	Fetal Thymus	thymus
13	chr1:225923000-225925400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:225923000-225925600	Enhancers	Adipose Nuclei	Adipose
15	chr1:225923000-225925600	Flanking Active TSS	A549	lung
16	chr1:225923000-225925800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:225923000-225925800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:225923000-225925800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:225923000-225925800	Enhancers	Fetal Muscle Trunk	muscle
20	chr1:225923000-225925800	Enhancers	Right Atrium	heart
21	chr1:225923000-225925800	Flanking Active TSS	Hela-S3	cervix
22	chr1:225923000-225925800	Enhancers	NH-A	brain
23	chr1:225923000-225926000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:225923000-225926000	Enhancers	Fetal Heart	heart
25	chr1:225923200-225925400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr1:225923200-225925600	Enhancers	HUVEC	blood vessel
27	chr1:225923400-225924800	Flanking Active TSS	Osteobl	bone
28	chr1:225923400-225925600	Enhancers	NHLF	lung
29	chr1:225923600-225925200	Enhancers	Brain Cingulate Gyrus	brain
30	chr1:225923800-225925000	Enhancers	Stomach Smooth Muscle	stomach
31	chr1:225923800-225925800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:225924000-225925000	Active TSS	Fetal Brain Male	brain
33	chr1:225924000-225925400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:225924000-225925600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:225924000-225925800	Enhancers	HMEC	breast
36	chr1:225924000-225925800	Enhancers	HSMMtube	muscle
37	chr1:225924200-225925400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:225924200-225925600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:225924200-225925800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:225924200-225925800	Enhancers	NHEK	skin
41	chr1:225924400-225924800	Weak transcription	Spleen	Spleen
42	chr1:225924400-225925800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:225924400-225925800	Enhancers	HSMM	muscle
44	chr1:225924600-225925000	Weak transcription	Placenta	Placenta
45	chr1:225924600-225925600	Weak transcription	Brain Germinal Matrix	brain
46	chr1:225924600-225925800	Enhancers	Lung	lung
47	chr1:225924600-225925800	Enhancers	HepG2	liver
48	chr1:225924600-225925800	Enhancers	NHDF-Ad	bronchial

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