Variant report

Variant	rs12485825
Chromosome Location	chr3:51705952-51705953
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	POLR2A	chr3:51704970-51706186	GM12878	blood:	n/a	n/a
2	USF1	chr3:51705656-51706142	ECC-1	luminal epithelium:	n/a	chr3:51705859-51705872 chr3:51705996-51706012
3	NRF1	chr3:51704810-51706666	SK-N-SH	brain:	n/a	chr3:51705859-51705868 chr3:51705235-51705246 chr3:51705163-51705177 chr3:51705217-51705228 chr3:51705166-51705175 chr3:51705263-51705274 chr3:51705166-51705177
4	POLR2A	chr3:51704829-51706272	MCF-7	breast:	n/a	n/a
5	POLR2A	chr3:51704884-51706176	SK-N-SH	brain:	n/a	n/a
6	MYBL2	chr3:51705688-51706171	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:51705001-51706273	K562	blood:	n/a	n/a
8	ZBTB7A	chr3:51705875-51706068	K562	blood:	n/a	n/a
9	EP300	chr3:51704998-51706090	GM12878	blood:	n/a	chr3:51705845-51705861 chr3:51705764-51705773
10	TAF1	chr3:51705790-51706092	K562	blood:	n/a	n/a
11	GTF2F1	chr3:51705834-51706000	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:51704870-51706245	HCT-116	colon:	n/a	n/a
13	MAX	chr3:51704953-51706188	A549	lung:	n/a	chr3:51705863-51705879 chr3:51705771-51705781 chr3:51705119-51705128 chr3:51705123-51705132
14	POLR2A	chr3:51705811-51706020	A549	lung:	n/a	n/a
15	MXI1	chr3:51705619-51705969	K562	blood:	n/a	n/a
16	POLR2A	chr3:51705833-51706132	HepG2	liver:	n/a	n/a
17	MAX	chr3:51704848-51706190	MCF-7	breast:	n/a	chr3:51705863-51705879 chr3:51705771-51705781 chr3:51705119-51705128 chr3:51705123-51705132
18	CTCF	chr3:51705860-51706010	SK-N-SH_RA	brain:	n/a	n/a
19	TCF7L2	chr3:51704961-51706084	HCT-116	colon:	n/a	n/a
20	TCF12	chr3:51704787-51706171	ECC-1	luminal epithelium:	n/a	chr3:51705450-51705457
21	MYC	chr3:51705000-51706111	K562	blood:	n/a	chr3:51705863-51705879 chr3:51705771-51705781 chr3:51705119-51705128 chr3:51705123-51705132
22	CTCF	chr3:51705820-51705970	GM12875	blood:	n/a	n/a
23	MYC	chr3:51705710-51706053	HepG2	liver:	n/a	chr3:51705863-51705879 chr3:51705771-51705781
24	HEY1	chr3:51705040-51706317	HepG2	liver:	n/a	chr3:51705162-51705177 chr3:51706260-51706275
25	POLR2A	chr3:51704824-51706185	H1-hESC	embryonic stem cell:	n/a	n/a
26	TAF1	chr3:51705709-51706135	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr3:51704738-51706189	HL-60	blood:	n/a	n/a
28	CTCF	chr3:51705935-51706019	MCF-7	breast:	n/a	n/a
29	POLR2A	chr3:51705764-51706102	U87	brain:	n/a	n/a
30	POLR2A	chr3:51705043-51706156	K562	blood:	n/a	n/a
31	TAF1	chr3:51705740-51706037	K562	blood:	n/a	n/a
32	RCOR1	chr3:51704839-51706186	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr3:51705628-51706302	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr3:51704856-51706329	GM18526	blood:	n/a	n/a
35	MYC	chr3:51704965-51706267	K562	blood:	n/a	chr3:51705863-51705879 chr3:51705771-51705781 chr3:51705119-51705128 chr3:51705123-51705132
36	TCF7L2	chr3:51704964-51705984	Hela-S3	cervix:	n/a	n/a
37	YY1	chr3:51705032-51705967	GM12878	blood:	n/a	chr3:51705762-51705771 chr3:51705410-51705419 chr3:51705145-51705159 chr3:51705850-51705861 chr3:51705853-51705862 chr3:51705841-51705855 chr3:51705956-51705967
38	POLR2A	chr3:51704963-51706228	HCT-116	colon:	n/a	n/a
39	MAX	chr3:51704855-51706080	K562	blood:	n/a	chr3:51705863-51705879 chr3:51705771-51705781 chr3:51705119-51705128 chr3:51705123-51705132
40	HEY1	chr3:51705752-51706068	HepG2	liver:	n/a	n/a
41	CTCF	chr3:51705946-51705966	GM19238	blood:	n/a	n/a
42	HA-E2F1	chr3:51704817-51706155	Hela-S3	cervix:	n/a	chr3:51705167-51705176 chr3:51705058-51705070
43	SIN3A	chr3:51704910-51706277	GM12878	blood:	n/a	chr3:51705991-51706004 chr3:51705457-51705470 chr3:51705847-51705858
44	POLR2A	chr3:51704684-51706405	GM18505	blood:	n/a	n/a
45	MAX	chr3:51705616-51706176	MCF-7	breast:	n/a	chr3:51705863-51705879 chr3:51705771-51705781
46	RELA	chr3:51705085-51706254	GM18951	blood:	n/a	n/a
47	TAL1	chr3:51705874-51706104	K562	blood:	n/a	n/a
48	ELF1	chr3:51705713-51706122	HepG2	liver:	n/a	chr3:51705853-51705862
49	UBTF	chr3:51705861-51706165	K562	blood:	n/a	n/a
50	CHD2	chr3:51704860-51706118	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:51705912-51705962	HCM	heart:	n/a
2	chr3:51705912-51705962	GM12878	blood:	n/a
3	chr3:51705912-51705962	NB4	blood:	n/a
4	chr3:51705912-51705962	A549	lung:	n/a
5	chr3:51705912-51705962	AG04449	skin:	fetal
6	chr3:51705912-51705962	HEK293	kidney:	embryo
7	chr3:51705912-51705962	SK-N-SH	brain:	n/a
8	chr3:51705912-51705962	HCPEpiC	choroid plexus:	n/a
9	chr3:51705912-51705962	Hepatocyte	liver:	n/a
10	chr3:51705912-51705962	HNPCEpiC	eye:	n/a
11	chr3:51705912-51705962	SK-N-MC	brain:	n/a
12	chr3:51705912-51705962	SKMC	muscle:	n/a
13	chr3:51705912-51705962	HRCEpiC	kidney:	n/a
14	chr3:51705912-51705962	HUVEC	blood vessel:	n/a
15	chr3:51705912-51705962	LNCaP	prostate:	n/a
16	chr3:51705912-51705962	HRE	kidney:	n/a
17	chr3:51705912-51705962	NHBE	bronchial:	n/a
18	chr3:51705912-51705962	HIPEpiC	eye:	n/a
19	chr3:51705912-51705962	PrEC	prostate:	n/a
20	chr3:51705912-51705962	HCT-116	colon:	n/a
21	chr3:51705912-51705962	H1-hESC	embryonic stem cell:	embryo
22	chr3:51705912-51705962	HEEpiC	esophagus:	n/a
23	chr3:51705912-51705962	HMEC	breast:	n/a
24	chr3:51705912-51705962	Hela-S3	cervix:	n/a
25	chr3:51705912-51705962	ECC-1	luminal epithelium:	n/a
26	chr3:51705912-51705962	K562	blood:	n/a
27	chr3:51705912-51705962	T-47D	breast:	n/a
28	chr3:51705912-51705962	ovcar-3	ovarian:	n/a
29	chr3:51705912-51705962	RPTEC	kidney:	n/a
30	chr3:51705912-51705962	HPAEpiC	pulmonary alveolar:	n/a
31	chr3:51705912-51705962	PANC-1	pancreas:	n/a
32	chr3:51705912-51705962	SAEC	small airway:	n/a
33	chr3:51705912-51705962	AG09319	gingival:	n/a
34	chr3:51705912-51705962	AG10803	skin:	n/a
35	chr3:51705912-51705962	IMR90	lung:	fetal
36	chr3:51705912-51705962	GM12892	blood:	n/a
37	chr3:51705912-51705962	HL-60	blood:	n/a
38	chr3:51705912-51705962	GM19239	blood:	n/a
39	chr3:51705912-51705962	AoSMC	blood vessel:	n/a
40	chr3:51705912-51705962	HCF	heart:	n/a
41	chr3:51705912-51705962	PFSK-1	brain:	n/a
42	chr3:51705912-51705962	NH-A	brain:	n/a
43	chr3:51705912-51705962	GM06990	blood:	n/a
44	chr3:51705912-51705962	NT2-D1	testis:	n/a
45	chr3:51705912-51705962	GM12891	blood:	n/a
46	chr3:51705912-51705962	NHDF-neo	bronchial:	n/a
47	chr3:51705912-51705962	BJ	skin:	n/a
48	chr3:51705912-51705962	AG09309	skin:	n/a
49	chr3:51705912-51705962	Caco-2	colon:	n/a
50	chr3:51705912-51705962	U87	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:51532457..51535099-chr3:51703667..51706623,4	MCF-7	breast:
2	chr3:51532560..51534895-chr3:51704003..51706915,3	K562	blood:
3	chr3:51703488..51706346-chr3:51714334..51716919,2	MCF-7	breast:
4	chr11:16759738..16760372-chr3:51705251..51705984,2	HCT-116	colon:
5	chr3:51533144..51535964-chr3:51704671..51707377,2	MCF-7	breast:
6	chr3:51704425..51707228-chr3:51714036..51717789,3	MCF-7	breast:
7	chr3:51704201..51711015-chr3:51712254..51717093,7	K562	blood:
8	chr3:51532096..51536424-chr3:51702408..51707498,7	K562	blood:
9	chr3:51702918..51706936-chr3:51707889..51711767,6	MCF-7	breast:

Variant related genes	Relation type
TEX264	TF binding region
TEX264	CpG island
ENSG00000164081	Chromatin interaction
ENSG00000145041	Chromatin interaction
ENSG00000110693	Chromatin interaction
ENSG00000110696	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11553574	0.88[ASN][1000 genomes]
rs12487957	0.81[ASN][1000 genomes]
rs12496340	0.94[ASN][1000 genomes]
rs13324384	0.88[ASN][1000 genomes]
rs4687592	0.91[ASN][1000 genomes]
rs4687599	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4687769	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs55706150	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs55872019	0.92[ASN][1000 genomes]
rs59955041	0.81[ASN][1000 genomes]
rs72951490	0.83[ASN][1000 genomes]
rs7375146	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs73834265	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS 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 target site	53 gene(s)	inside rSNPs	diseases
2	nsv965167	chr3:51702892-51707059	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1814919	chr3:51703488-51752684	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51703000-51707800	Enhancers	Fetal Heart	heart
2	chr3:51704400-51706400	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr3:51704400-51706800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:51704400-51706800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:51704400-51706800	Flanking Active TSS	HMEC	breast
6	chr3:51704600-51706000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:51704600-51706000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:51704600-51706000	Active TSS	NH-A	brain
9	chr3:51704600-51706200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:51704600-51706200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:51704600-51706400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr3:51704600-51706600	Active TSS	H1 Cell Line	embryonic stem cell
13	chr3:51704800-51706000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:51704800-51706000	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr3:51704800-51706000	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr3:51704800-51706200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:51704800-51706200	Active TSS	Aorta	Aorta
18	chr3:51704800-51706200	Active TSS	Lung	lung
19	chr3:51704800-51706400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:51704800-51706400	Active TSS	H9 Cell Line	embryonic stem cell
21	chr3:51704800-51706400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:51704800-51706400	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr3:51704800-51706400	Active TSS	Ovary	ovary
24	chr3:51704800-51706400	Active TSS	NHDF-Ad	bronchial
25	chr3:51704800-51706600	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr3:51704800-51706600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:51705000-51706000	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr3:51705000-51706000	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr3:51705000-51706000	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr3:51705000-51706000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:51705000-51706000	Active TSS	Primary T cells from cord blood	blood
32	chr3:51705000-51706000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:51705000-51706000	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr3:51705000-51706000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:51705000-51706000	Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr3:51705000-51706000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr3:51705000-51706000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:51705000-51706000	Active TSS	Muscle Satellite Cultured Cells	--
39	chr3:51705000-51706000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:51705000-51706000	Active TSS	Liver	Liver
41	chr3:51705000-51706000	Active TSS	Brain Anterior Caudate	brain
42	chr3:51705000-51706000	Active TSS	Brain Cingulate Gyrus	brain
43	chr3:51705000-51706000	Active TSS	Brain Hippocampus Middle	brain
44	chr3:51705000-51706000	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr3:51705000-51706000	Active TSS	Brain Substantia Nigra	brain
46	chr3:51705000-51706000	Active TSS	Duodenum Mucosa	Duodenum
47	chr3:51705000-51706000	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr3:51705000-51706000	Active TSS	Esophagus	oesophagus
49	chr3:51705000-51706000	Active TSS	Fetal Intestine Large	intestine
50	chr3:51705000-51706000	Active TSS	Fetal Intestine Small	intestine

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