Variant report

Variant	rs72953417
Chromosome Location	chr3:51705345-51705346
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	CEBPD	chr3:51705071-51705427	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:51704970-51706186	GM12878	blood:	n/a	n/a
3	PAX5	chr3:51704987-51705660	GM12892	blood:	n/a	chr3:51705167-51705176
4	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
5	POLR2A	chr3:51704829-51706272	MCF-7	breast:	n/a	n/a
6	POLR2A	chr3:51704884-51706176	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr3:51705001-51706273	K562	blood:	n/a	n/a
8	TAF1	chr3:51705046-51705477	H1-hESC	embryonic stem cell:	n/a	n/a
9	EP300	chr3:51704998-51706090	GM12878	blood:	n/a	chr3:51705845-51705861 chr3:51705764-51705773
10	ETS1	chr3:51705190-51705465	A549	lung:	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	TAF1	chr3:51705078-51705428	PFSK-1	brain:	n/a	n/a
14	YY1	chr3:51705054-51705368	K562	blood:	n/a	chr3:51705145-51705159
15	MAX	chr3:51704848-51706190	MCF-7	breast:	n/a	chr3:51705863-51705879 chr3:51705771-51705781 chr3:51705119-51705128 chr3:51705123-51705132
16	ELF1	chr3:51705313-51705627	HepG2	liver:	n/a	chr3:51705524-51705536
17	TCF7L2	chr3:51704961-51706084	HCT-116	colon:	n/a	n/a
18	TCF12	chr3:51704787-51706171	ECC-1	luminal epithelium:	n/a	chr3:51705450-51705457
19	MYC	chr3:51705000-51706111	K562	blood:	n/a	chr3:51705863-51705879 chr3:51705771-51705781 chr3:51705119-51705128 chr3:51705123-51705132
20	HEY1	chr3:51705040-51706317	HepG2	liver:	n/a	chr3:51705162-51705177 chr3:51706260-51706275
21	EGR1	chr3:51705037-51705382	GM12878	blood:	n/a	chr3:51705166-51705175 chr3:51705167-51705176 chr3:51705203-51705217
22	POLR2A	chr3:51704824-51706185	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr3:51704738-51706189	HL-60	blood:	n/a	n/a
24	HDAC2	chr3:51704902-51705573	K562	blood:	n/a	chr3:51705166-51705175
25	ZNF384	chr3:51705124-51705442	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:51705043-51706156	K562	blood:	n/a	n/a
27	RCOR1	chr3:51704839-51706186	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr3:51705055-51705474	HepG2	liver:	n/a	n/a
29	FOSL2	chr3:51704907-51705476	HepG2	liver:	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	TCF7L2	chr3:51704964-51705984	Hela-S3	cervix:	n/a	n/a
33	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
34	POLR2A	chr3:51704963-51706228	HCT-116	colon:	n/a	n/a
35	MAX	chr3:51704855-51706080	K562	blood:	n/a	chr3:51705863-51705879 chr3:51705771-51705781 chr3:51705119-51705128 chr3:51705123-51705132
36	HEY1	chr3:51705122-51705698	HepG2	liver:	n/a	chr3:51705162-51705177
37	RUNX3	chr3:51704784-51705717	GM12878	blood:	n/a	n/a
38	HA-E2F1	chr3:51704817-51706155	Hela-S3	cervix:	n/a	chr3:51705167-51705176 chr3:51705058-51705070
39	SIN3A	chr3:51704910-51706277	GM12878	blood:	n/a	chr3:51705991-51706004 chr3:51705457-51705470 chr3:51705847-51705858
40	POLR2A	chr3:51704684-51706405	GM18505	blood:	n/a	n/a
41	RELA	chr3:51705085-51706254	GM18951	blood:	n/a	n/a
42	CHD2	chr3:51704860-51706118	Hela-S3	cervix:	n/a	n/a
43	SRF	chr3:51705068-51705372	GM12878	blood:	n/a	chr3:51705307-51705317
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	POLR2A	chr3:51704810-51706190	GM12878	blood:	n/a	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	chr3:51705086..51705705-chr9:86536186..86536829,2	HCT-116	colon:
5	chr11:16759738..16760372-chr3:51705251..51705984,2	HCT-116	colon:
6	chr3:51533144..51535964-chr3:51704671..51707377,2	MCF-7	breast:
7	chr3:51704425..51707228-chr3:51714036..51717789,3	MCF-7	breast:
8	chr3:51704201..51711015-chr3:51712254..51717093,7	K562	blood:
9	chr3:51532096..51536424-chr3:51702408..51707498,7	K562	blood:
10	chr3:51702918..51706936-chr3:51707889..51711767,6	MCF-7	breast:

Variant related genes	Relation type
TEX264	TF binding region
ENSG00000110693	Chromatin interaction
ENSG00000145041	Chromatin interaction
ENSG00000164081	Chromatin interaction
ENSG00000110696	Chromatin interaction
ENSG00000165115	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs12330534	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13314120	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13321674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13433729	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17051799	1.00[AMR][1000 genomes]
rs17051832	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17081501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28421789	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28452990	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28457212	1.00[AMR][1000 genomes]
rs28653367	1.00[AMR][1000 genomes]
rs2883900	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4549265	1.00[AMR][1000 genomes]
rs56942057	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59064710	1.00[ASN][1000 genomes]
rs59525691	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60823123	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61440245	1.00[ASN][1000 genomes]
rs61737032	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951441	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951452	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951472	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951485	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951486	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953413	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953419	1.00[ASN][1000 genomes]
rs72953421	1.00[ASN][1000 genomes]
rs72953423	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953429	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7627636	1.00[ASN][1000 genomes]
rs904144	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9311470	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9808940	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9809757	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812008	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812682	1.00[ASN][1000 genomes]
rs9815684	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9816075	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9824779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9826664	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9827665	1.00[AMR][1000 genomes]
rs9827917	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838294	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838942	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838994	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839516	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839608	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9842066	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9844541	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9846343	1.00[ASN][1000 genomes]
rs9855809	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9857893	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9858497	1.00[AMR][1000 genomes]
rs9864213	1.00[AMR][1000 genomes]
rs9864952	1.00[ASN][1000 genomes]
rs9866513	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9866604	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9870147	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9875460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9880050	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9880909	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881402	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881844	1.00[AMR][1000 genomes]
rs9882601	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9990341	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];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	chr3:51704000-51705600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:51704400-51706400	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr3:51704400-51706800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:51704400-51706800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:51704400-51706800	Flanking Active TSS	HMEC	breast
7	chr3:51704600-51706000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:51704600-51706000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:51704600-51706000	Active TSS	NH-A	brain
10	chr3:51704600-51706200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:51704600-51706200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:51704600-51706400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr3:51704600-51706600	Active TSS	H1 Cell Line	embryonic stem cell
14	chr3:51704800-51706000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:51704800-51706000	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr3:51704800-51706000	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr3:51704800-51706200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:51704800-51706200	Active TSS	Aorta	Aorta
19	chr3:51704800-51706200	Active TSS	Lung	lung
20	chr3:51704800-51706400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:51704800-51706400	Active TSS	H9 Cell Line	embryonic stem cell
22	chr3:51704800-51706400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:51704800-51706400	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr3:51704800-51706400	Active TSS	Ovary	ovary
25	chr3:51704800-51706400	Active TSS	NHDF-Ad	bronchial
26	chr3:51704800-51706600	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr3:51704800-51706600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:51705000-51705400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr3:51705000-51705400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:51705000-51705400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr3:51705000-51705400	Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr3:51705000-51705400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:51705000-51705400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr3:51705000-51705400	Transcr. at gene 5' and 3'	Right Atrium	heart
35	chr3:51705000-51705400	Active TSS	HUVEC	blood vessel
36	chr3:51705000-51705600	Active TSS	Colonic Mucosa	Colon
37	chr3:51705000-51705800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:51705000-51705800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:51705000-51705800	Active TSS	Placenta Amnion	Placenta Amnion
40	chr3:51705000-51706000	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr3:51705000-51706000	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr3:51705000-51706000	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr3:51705000-51706000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:51705000-51706000	Active TSS	Primary T cells from cord blood	blood
45	chr3:51705000-51706000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:51705000-51706000	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr3:51705000-51706000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:51705000-51706000	Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr3:51705000-51706000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr3:51705000-51706000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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