Variant report

Variant	rs62251110
Chromosome Location	chr3:28370419-28370420
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	SMC3	chr3:28370028-28370421	HepG2	liver:	n/a	n/a
2	CTCF	chr3:28370025-28370450	A549	lung:	n/a	chr3:28370227-28370248
3	RAD21	chr3:28369957-28370467	HCT-116	colon:	n/a	chr3:28370151-28370163 chr3:28370236-28370245
4	POLR2A	chr3:28360241-28371279	K562	blood:	n/a	n/a
5	RAD21	chr3:28369953-28370432	SK-N-SH_RA	brain:	n/a	chr3:28370151-28370163 chr3:28370236-28370245
6	RFX5	chr3:28370051-28370432	Hela-S3	cervix:	n/a	n/a
7	RAD21	chr3:28369921-28370489	A549	lung:	n/a	chr3:28370151-28370163 chr3:28370236-28370245
8	SMC3	chr3:28369979-28370489	GM12878	blood:	n/a	n/a
9	RAD21	chr3:28369782-28370608	SK-N-SH	brain:	n/a	chr3:28370151-28370163 chr3:28370236-28370245
10	CTCF	chr3:28369962-28370476	K562	blood:	n/a	chr3:28370227-28370248
11	RAD21	chr3:28370053-28370440	H1-hESC	embryonic stem cell:	n/a	chr3:28370151-28370163 chr3:28370236-28370245
12	CTCF	chr3:28370320-28370470	HFF	foreskin:	n/a	n/a
13	CTCF	chr3:28370380-28370530	GM12864	blood:	n/a	n/a
14	SMC3	chr3:28369987-28370472	Hela-S3	cervix:	n/a	n/a
15	RAD21	chr3:28369997-28370471	ECC-1	luminal epithelium:	n/a	chr3:28370151-28370163 chr3:28370236-28370245
16	RAD21	chr3:28370000-28370422	Hela-S3	cervix:	n/a	chr3:28370151-28370163 chr3:28370236-28370245
17	CTCF	chr3:28370280-28370430	HCT-116	colon:	n/a	n/a
18	JUN	chr3:28369784-28370425	K562	blood:	n/a	n/a
19	CTCF	chr3:28369745-28370584	A549	lung:	n/a	chr3:28370227-28370248
20	CTCF	chr3:28369812-28370471	GM12878	blood:	n/a	chr3:28370227-28370248
21	CTCF	chr3:28369887-28370575	IMR90	lung:	n/a	chr3:28370227-28370248
22	CTCF	chr3:28369549-28370753	SK-N-SH	brain:	n/a	chr3:28370227-28370248
23	E2F4	chr3:28370094-28370420	MCF10A-Er-Src	breast:	n/a	n/a
24	RAD21	chr3:28369950-28370480	H1-hESC	embryonic stem cell:	n/a	chr3:28370151-28370163 chr3:28370236-28370245
25	RAD21	chr3:28369986-28370509	A549	lung:	n/a	chr3:28370151-28370163 chr3:28370236-28370245
26	CTCF	chr3:28369932-28370536	HCT-116	colon:	n/a	chr3:28370227-28370248
27	RAD21	chr3:28369975-28370430	GM12878	blood:	n/a	chr3:28370151-28370163 chr3:28370236-28370245
28	MAFK	chr3:28370211-28371016	HepG2	liver:	n/a	chr3:28370886-28370900 chr3:28370887-28370898 chr3:28370887-28370898 chr3:28370888-28370899
29	RAD21	chr3:28369890-28370500	HepG2	liver:	n/a	chr3:28370151-28370163 chr3:28370236-28370245
30	ZNF143	chr3:28370063-28370434	GM12878	blood:	n/a	n/a
31	RAD21	chr3:28369908-28370492	HCT-116	colon:	n/a	chr3:28370151-28370163 chr3:28370236-28370245
32	RAD21	chr3:28369865-28370452	HepG2	liver:	n/a	chr3:28370151-28370163 chr3:28370236-28370245
33	RAD21	chr3:28370035-28370446	H1-hESC	embryonic stem cell:	n/a	chr3:28370151-28370163 chr3:28370236-28370245

No.	Distal block	Cell Line	Cell type
1	chr3:28326930..28329184-chr3:28369613..28371259,2	K562	blood:
2	chr3:28370043..28372109-chr3:28386223..28389083,2	MCF-7	breast:
3	chr3:28370176..28372872-chr3:28373857..28375722,2	MCF-7	breast:
4	chr3:28370239..28373025-chr3:28374820..28376811,3	K562	blood:
5	chr3:27984407..27984923-chr3:28369790..28370658,2	MCF-7	breast:

Variant related genes	Relation type
AZI2	TF binding region
ENSG00000163512	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10510610	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11716132	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12106746	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12106806	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12107556	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12107561	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374021	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485652	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12491905	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12493720	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12493797	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13068978	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13069450	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13089663	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13090951	0.91[EUR][1000 genomes]
rs13095609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13099977	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1588669	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1599951	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17639954	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1870258	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2125205	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34335277	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34463163	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34539152	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34637008	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34914936	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35194037	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35374336	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36106945	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4393865	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4552313	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680912	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56058287	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62251112	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251132	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551254	0.81[EUR][1000 genomes]
rs6799435	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6805638	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7624015	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7624111	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9968098	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28317600-28380000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:28317600-28389400	Weak transcription	Esophagus	oesophagus
3	chr3:28343800-28383800	Weak transcription	Aorta	Aorta
4	chr3:28349800-28389400	Weak transcription	Gastric	stomach
5	chr3:28350000-28376800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:28356800-28376800	Weak transcription	Ovary	ovary
7	chr3:28358600-28386400	Weak transcription	Thymus	Thymus
8	chr3:28358800-28389000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:28359600-28377200	Weak transcription	Brain Anterior Caudate	brain
10	chr3:28360400-28383800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:28360400-28387400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:28361600-28382200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:28362800-28382400	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:28362800-28387800	Weak transcription	HUVEC	blood vessel
15	chr3:28363200-28377200	Weak transcription	Fetal Kidney	kidney
16	chr3:28363600-28389000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:28363800-28380000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:28363800-28389600	Weak transcription	Spleen	Spleen
19	chr3:28364000-28388400	Weak transcription	Fetal Brain Female	brain
20	chr3:28364200-28376800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:28364400-28373200	Weak transcription	Brain Germinal Matrix	brain
22	chr3:28364800-28377000	Weak transcription	Brain Substantia Nigra	brain
23	chr3:28364800-28382400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:28365400-28383800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:28365400-28389400	Weak transcription	Lung	lung
26	chr3:28366000-28388600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:28366200-28376800	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:28366200-28378000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:28366200-28389400	Weak transcription	Colonic Mucosa	Colon
30	chr3:28366400-28389200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:28366800-28379000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:28367000-28376800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:28367000-28376800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:28367000-28384200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:28367000-28388800	Weak transcription	Brain Angular Gyrus	brain
36	chr3:28367000-28389000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:28367200-28376800	Weak transcription	Fetal Muscle Leg	muscle
38	chr3:28367200-28377000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr3:28367200-28379000	Weak transcription	HSMMtube	muscle
40	chr3:28367200-28384000	Weak transcription	Fetal Heart	heart
41	chr3:28367200-28387800	Weak transcription	Fetal Brain Male	brain
42	chr3:28367200-28388800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr3:28367200-28389400	Weak transcription	Pancreas	Pancrea
44	chr3:28367400-28376800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:28367400-28388800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:28367600-28372800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:28367600-28377000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:28368000-28373600	Weak transcription	Liver	Liver
49	chr3:28368200-28376600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:28368200-28377000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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