Variant report

Variant	rs72953419
Chromosome Location	chr3:51706021-51706022
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	POLR2A	chr3:51704870-51706245	HCT-116	colon:	n/a	n/a
12	MAX	chr3:51704953-51706188	A549	lung:	n/a	chr3:51705863-51705879 chr3:51705771-51705781 chr3:51705119-51705128 chr3:51705123-51705132
13	CTCF	chr3:51705966-51706023	GM19239	blood:	n/a	n/a
14	POLR2A	chr3:51705833-51706132	HepG2	liver:	n/a	n/a
15	MAX	chr3:51704848-51706190	MCF-7	breast:	n/a	chr3:51705863-51705879 chr3:51705771-51705781 chr3:51705119-51705128 chr3:51705123-51705132
16	TCF7L2	chr3:51704961-51706084	HCT-116	colon:	n/a	n/a
17	TCF12	chr3:51704787-51706171	ECC-1	luminal epithelium:	n/a	chr3:51705450-51705457
18	MYC	chr3:51705000-51706111	K562	blood:	n/a	chr3:51705863-51705879 chr3:51705771-51705781 chr3:51705119-51705128 chr3:51705123-51705132
19	MYC	chr3:51705710-51706053	HepG2	liver:	n/a	chr3:51705863-51705879 chr3:51705771-51705781
20	HEY1	chr3:51705040-51706317	HepG2	liver:	n/a	chr3:51705162-51705177 chr3:51706260-51706275
21	POLR2A	chr3:51704824-51706185	H1-hESC	embryonic stem cell:	n/a	n/a
22	TAF1	chr3:51705709-51706135	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr3:51704738-51706189	HL-60	blood:	n/a	n/a
24	POLR2A	chr3:51705764-51706102	U87	brain:	n/a	n/a
25	CTCF	chr3:51705964-51706030	MCF-7	breast:	n/a	n/a
26	POLR2A	chr3:51705043-51706156	K562	blood:	n/a	n/a
27	TAF1	chr3:51705740-51706037	K562	blood:	n/a	n/a
28	RCOR1	chr3:51704839-51706186	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr3:51705628-51706302	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr3:51704856-51706329	GM18526	blood:	n/a	n/a
31	MYC	chr3:51704965-51706267	K562	blood:	n/a	chr3:51705863-51705879 chr3:51705771-51705781 chr3:51705119-51705128 chr3:51705123-51705132
32	POLR2A	chr3:51704963-51706228	HCT-116	colon:	n/a	n/a
33	MAX	chr3:51704855-51706080	K562	blood:	n/a	chr3:51705863-51705879 chr3:51705771-51705781 chr3:51705119-51705128 chr3:51705123-51705132
34	HEY1	chr3:51705752-51706068	HepG2	liver:	n/a	n/a
35	HA-E2F1	chr3:51704817-51706155	Hela-S3	cervix:	n/a	chr3:51705167-51705176 chr3:51705058-51705070
36	SIN3A	chr3:51704910-51706277	GM12878	blood:	n/a	chr3:51705991-51706004 chr3:51705457-51705470 chr3:51705847-51705858
37	POLR2A	chr3:51704684-51706405	GM18505	blood:	n/a	n/a
38	MAX	chr3:51705616-51706176	MCF-7	breast:	n/a	chr3:51705863-51705879 chr3:51705771-51705781
39	RELA	chr3:51705085-51706254	GM18951	blood:	n/a	n/a
40	TAL1	chr3:51705874-51706104	K562	blood:	n/a	n/a
41	ELF1	chr3:51705713-51706122	HepG2	liver:	n/a	chr3:51705853-51705862
42	UBTF	chr3:51705861-51706165	K562	blood:	n/a	n/a
43	CHD2	chr3:51704860-51706118	Hela-S3	cervix:	n/a	n/a
44	BHLHE40	chr3:51704957-51706193	HepG2	liver:	n/a	chr3:51705859-51705872 chr3:51705525-51705541 chr3:51705996-51706012
45	POLR2A	chr3:51704953-51706316	K562	blood:	n/a	n/a
46	ELF1	chr3:51705331-51706282	K562	blood:	n/a	chr3:51705524-51705536 chr3:51705853-51705862
47	ELF1	chr3:51704931-51706067	K562	blood:	n/a	chr3:51705524-51705536 chr3:51705147-51705159 chr3:51705853-51705862
48	POLR2A	chr3:51704948-51706193	ProgFib	skin:	n/a	n/a
49	YY1	chr3:51704893-51706147	HepG2	liver:	n/a	chr3:51705762-51705771 chr3:51705410-51705419 chr3:51705145-51705159 chr3:51705850-51705861 chr3:51705853-51705862 chr3:51705841-51705855 chr3:51705956-51705967
50	YY1	chr3:51705667-51706169	H1-hESC	embryonic stem cell:	n/a	chr3:51705762-51705771 chr3:51705850-51705861 chr3:51705853-51705862 chr3:51705841-51705855 chr3:51705956-51705967

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	chr3:51533144..51535964-chr3:51704671..51707377,2	MCF-7	breast:
5	chr3:51704425..51707228-chr3:51714036..51717789,3	MCF-7	breast:
6	chr3:51704201..51711015-chr3:51712254..51717093,7	K562	blood:
7	chr3:51532096..51536424-chr3:51702408..51707498,7	K562	blood:
8	chr3:51702918..51706936-chr3:51707889..51711767,6	MCF-7	breast:

Variant related genes	Relation type
TEX264	TF binding region
ENSG00000145041	Chromatin interaction
ENSG00000164081	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs12330534	1.00[ASN][1000 genomes]
rs13314120	1.00[ASN][1000 genomes]
rs13321674	1.00[ASN][1000 genomes]
rs13433729	1.00[ASN][1000 genomes]
rs17051802	1.00[AMR][1000 genomes]
rs17051832	1.00[ASN][1000 genomes]
rs17081501	1.00[ASN][1000 genomes]
rs28421789	1.00[ASN][1000 genomes]
rs28452990	1.00[ASN][1000 genomes]
rs2883900	1.00[ASN][1000 genomes]
rs4280628	1.00[AMR][1000 genomes]
rs4555511	1.00[AMR][1000 genomes]
rs56942057	1.00[ASN][1000 genomes]
rs57019473	1.00[AMR][1000 genomes]
rs58075772	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58807639	1.00[AMR][1000 genomes]
rs59064710	1.00[ASN][1000 genomes]
rs59307262	1.00[AMR][1000 genomes]
rs59525691	1.00[ASN][1000 genomes]
rs60497133	1.00[AMR][1000 genomes]
rs60823123	1.00[ASN][1000 genomes]
rs61440245	1.00[ASN][1000 genomes]
rs61452834	1.00[AMR][1000 genomes]
rs61737032	1.00[ASN][1000 genomes]
rs72945711	1.00[AMR][1000 genomes]
rs72945738	1.00[AMR][1000 genomes]
rs72945741	1.00[AMR][1000 genomes]
rs72951441	1.00[ASN][1000 genomes]
rs72951452	1.00[ASN][1000 genomes]
rs72951454	1.00[AMR][1000 genomes]
rs72951466	1.00[AMR][1000 genomes]
rs72951469	1.00[AMR][1000 genomes]
rs72951472	1.00[ASN][1000 genomes]
rs72951474	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951478	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951485	1.00[ASN][1000 genomes]
rs72951486	1.00[ASN][1000 genomes]
rs72951489	1.00[AMR][1000 genomes]
rs72953404	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72953413	1.00[ASN][1000 genomes]
rs72953417	1.00[ASN][1000 genomes]
rs72953421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953423	1.00[ASN][1000 genomes]
rs72953429	1.00[ASN][1000 genomes]
rs7627636	1.00[ASN][1000 genomes]
rs904144	1.00[ASN][1000 genomes]
rs9311470	1.00[ASN][1000 genomes]
rs9808940	1.00[ASN][1000 genomes]
rs9809757	1.00[ASN][1000 genomes]
rs9812008	1.00[ASN][1000 genomes]
rs9812682	1.00[ASN][1000 genomes]
rs9815684	1.00[ASN][1000 genomes]
rs9816075	1.00[ASN][1000 genomes]
rs9824779	1.00[ASN][1000 genomes]
rs9826664	1.00[ASN][1000 genomes]
rs9827917	1.00[ASN][1000 genomes]
rs9838294	1.00[ASN][1000 genomes]
rs9838942	1.00[ASN][1000 genomes]
rs9838994	1.00[ASN][1000 genomes]
rs9839516	1.00[ASN][1000 genomes]
rs9839608	1.00[ASN][1000 genomes]
rs9842066	1.00[ASN][1000 genomes]
rs9844541	1.00[ASN][1000 genomes]
rs9846343	1.00[ASN][1000 genomes]
rs9855809	1.00[ASN][1000 genomes]
rs9857893	1.00[ASN][1000 genomes]
rs9864952	1.00[ASN][1000 genomes]
rs9866513	1.00[ASN][1000 genomes]
rs9866604	1.00[ASN][1000 genomes]
rs9870147	1.00[ASN][1000 genomes]
rs9875460	1.00[ASN][1000 genomes]
rs9880050	1.00[ASN][1000 genomes]
rs9880909	1.00[ASN][1000 genomes]
rs9881402	1.00[ASN][1000 genomes]
rs9882601	1.00[ASN][1000 genomes]
rs9990341	1.00[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	chr3:51704600-51706200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:51704600-51706200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:51704600-51706400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr3:51704600-51706600	Active TSS	H1 Cell Line	embryonic stem cell
10	chr3:51704800-51706200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:51704800-51706200	Active TSS	Aorta	Aorta
12	chr3:51704800-51706200	Active TSS	Lung	lung
13	chr3:51704800-51706400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:51704800-51706400	Active TSS	H9 Cell Line	embryonic stem cell
15	chr3:51704800-51706400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:51704800-51706400	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr3:51704800-51706400	Active TSS	Ovary	ovary
18	chr3:51704800-51706400	Active TSS	NHDF-Ad	bronchial
19	chr3:51704800-51706600	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr3:51704800-51706600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:51705000-51706200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr3:51705000-51706200	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr3:51705000-51706200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:51705000-51706200	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr3:51705000-51706200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:51705000-51706200	Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr3:51705000-51706200	Active TSS	Colon Smooth Muscle	Colon
28	chr3:51705000-51706200	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr3:51705000-51706200	Active TSS	Right Ventricle	heart
30	chr3:51705000-51706200	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr3:51705000-51706200	Active TSS	Thymus	Thymus
32	chr3:51705000-51706200	Active TSS	GM12878-XiMat	blood
33	chr3:51705000-51706200	Active TSS	K562	blood
34	chr3:51705000-51706400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:51705000-51706400	Active TSS	Brain Angular Gyrus	brain
36	chr3:51705000-51706400	Active TSS	Gastric	stomach
37	chr3:51705000-51706600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:51705000-51706600	Enhancers	Fetal Brain Male	brain
39	chr3:51705000-51706600	Active TSS	Fetal Brain Female	brain
40	chr3:51705000-51706600	Active TSS	Fetal Kidney	kidney
41	chr3:51705000-51706600	Active TSS	A549	lung
42	chr3:51705000-51706600	Active TSS	HSMM	muscle
43	chr3:51705200-51706200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:51705200-51706200	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:51705200-51706200	Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr3:51705200-51706200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:51705200-51706200	Active TSS	Small Intestine	intestine
48	chr3:51705200-51706200	Active TSS	Spleen	Spleen
49	chr3:51705400-51706600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:51705400-51706600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland

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