Variant report

Variant	rs72818493
Chromosome Location	chr2:48539589-48539590
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	ARID3A	chr2:48539414-48539593	HepG2	liver:	n/a	chr2:48539471-48539487
2	FOSL1	chr2:48539055-48539703	HCT-116	colon:	n/a	n/a
3	FOS	chr2:48539096-48539817	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr2:48539144-48539720	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr2:48539441-48539745	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:48539447-48539740	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr2:48539171-48539919	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr2:48538991-48539749	MCF10A-Er-Src	breast:	n/a	chr2:48539309-48539320 chr2:48539191-48539205 chr2:48539198-48539205
9	FOS	chr2:48539148-48539822	MCF10A-Er-Src	breast:	n/a	n/a
10	CEBPB	chr2:48539544-48539593	H1-hESC	embryonic stem cell:	n/a	n/a
11	FOSL2	chr2:48539113-48539629	MCF-7	breast:	n/a	n/a
12	STAT3	chr2:48539066-48539942	MCF10A-Er-Src	breast:	n/a	chr2:48539309-48539320 chr2:48539191-48539205 chr2:48539198-48539205
13	MYC	chr2:48539246-48539890	MCF10A-Er-Src	breast:	n/a	n/a
14	STAT3	chr2:48539241-48539610	Hela-S3	cervix:	n/a	chr2:48539309-48539320
15	GATA3	chr2:48539023-48539646	SK-N-SH	brain:	n/a	n/a
16	SMC3	chr2:48539172-48539733	Hela-S3	cervix:	n/a	n/a
17	GATA3	chr2:48539108-48539715	SK-N-SH	brain:	n/a	n/a
18	RAD21	chr2:48539186-48539596	Hela-S3	cervix:	n/a	n/a
19	GATA3	chr2:48538871-48539923	MCF-7	breast:	n/a	n/a
20	MYC	chr2:48539142-48539847	MCF10A-Er-Src	breast:	n/a	n/a
21	STAT3	chr2:48539043-48539818	MCF10A-Er-Src	breast:	n/a	chr2:48539309-48539320 chr2:48539191-48539205 chr2:48539198-48539205
22	CEBPB	chr2:48539228-48539812	MCF-7	breast:	n/a	n/a
23	EP300	chr2:48539098-48539702	Hela-S3	cervix:	n/a	chr2:48539272-48539286
24	GATA3	chr2:48539094-48539767	MCF-7	breast:	n/a	n/a
25	CEBPB	chr2:48539410-48539747	IMR90	lung:	n/a	n/a
26	TCF7L2	chr2:48539264-48539848	Hela-S3	cervix:	n/a	n/a
27	GATA3	chr2:48539277-48539704	MCF-7	breast:	n/a	n/a
28	POLR2A	chr2:48539070-48543442	MCF10A-Er-Src	breast:	n/a	n/a
29	SIN3AK20	chr2:48539062-48539868	MCF-7	breast:	n/a	n/a
30	E2F4	chr2:48539332-48539890	MCF10A-Er-Src	breast:	n/a	n/a
31	FOS	chr2:48539124-48539889	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:48539557..48542081-chr2:48666297..48668955,4	MCF-7	breast:
2	chr2:48499034..48501158-chr2:48538819..48540781,2	K562	blood:
3	chr2:48515255..48518583-chr2:48539283..48541492,3	K562	blood:
4	chr2:48131515..48133334-chr2:48537826..48539696,2	MCF-7	breast:
5	chr2:48532704..48536258-chr2:48538581..48541257,5	K562	blood:
6	chr2:48538070..48539747-chr2:48539750..48541788,2	MCF-7	breast:

Variant related genes	Relation type
FOXN2	TF binding region
ENSG00000162869	Chromatin interaction
ENSG00000272663	Chromatin interaction
ENSG00000138081	Chromatin interaction
ENSG00000233230	Chromatin interaction
ENSG00000170802	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10153773	0.85[ASN][1000 genomes]
rs10174717	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10180295	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10186237	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10193072	0.98[ASN][1000 genomes]
rs10199431	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10208124	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11676168	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11682044	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11682931	0.81[EUR][1000 genomes]
rs11685861	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11690690	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12616792	0.87[ASN][1000 genomes]
rs12713008	0.87[ASN][1000 genomes]
rs12713009	0.87[ASN][1000 genomes]
rs13383364	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13385535	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13386751	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13387171	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13388291	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13392004	0.83[EUR][1000 genomes]
rs13426834	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13432998	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2471405	0.85[ASN][1000 genomes]
rs28806843	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28841370	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4290706	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4344965	0.80[EUR][1000 genomes]
rs4411759	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4547573	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4641990	0.90[ASN][1000 genomes]
rs56352447	0.94[ASN][1000 genomes]
rs57668696	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58660534	0.89[ASN][1000 genomes]
rs59264464	0.90[ASN][1000 genomes]
rs59412192	0.90[ASN][1000 genomes]
rs59761994	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60677957	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62136987	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62137001	0.89[ASN][1000 genomes]
rs62137002	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62137003	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62137005	0.89[ASN][1000 genomes]
rs62137006	0.89[ASN][1000 genomes]
rs62137007	0.89[ASN][1000 genomes]
rs62137008	0.87[ASN][1000 genomes]
rs62137009	0.87[ASN][1000 genomes]
rs62137015	0.81[EUR][1000 genomes]
rs62138801	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545027	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545028	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545029	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545030	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545034	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545035	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545036	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6712029	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6743757	0.82[EUR][1000 genomes]
rs6757206	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72820405	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72887649	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7340322	0.88[ASN][1000 genomes]
rs7562816	0.83[EUR][1000 genomes]
rs7568960	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7574125	0.83[ASN][1000 genomes]
rs7579932	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7600794	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7606104	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9309152	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48530200-48540200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:48533000-48539800	Weak transcription	Primary B cells from cord blood	blood
3	chr2:48534400-48540200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:48534600-48540200	Weak transcription	Adipose Nuclei	Adipose
5	chr2:48534600-48540200	Weak transcription	NHDF-Ad	bronchial
6	chr2:48534800-48539600	Weak transcription	Placenta	Placenta
7	chr2:48534800-48539600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:48534800-48539600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:48535600-48540400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:48535800-48539600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr2:48535800-48539600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:48538400-48540400	Enhancers	HepG2	liver
13	chr2:48538400-48540600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:48538600-48540400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:48538600-48540800	Enhancers	Fetal Intestine Large	intestine
16	chr2:48538800-48540200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:48538800-48541200	Enhancers	NHEK	skin
18	chr2:48539000-48540200	Enhancers	Liver	Liver
19	chr2:48539000-48540400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:48539000-48541000	Enhancers	Fetal Intestine Small	intestine
21	chr2:48539200-48539600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr2:48539200-48539800	Enhancers	Hela-S3	cervix
23	chr2:48539200-48540000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:48539200-48540200	Enhancers	Primary T cells from cord blood	blood
25	chr2:48539200-48540200	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr2:48539200-48540200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr2:48539200-48540200	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr2:48539200-48540200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr2:48539200-48541000	Enhancers	HMEC	breast
30	chr2:48539400-48540200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr2:48539400-48540200	Enhancers	Duodenum Mucosa	Duodenum
32	chr2:48539400-48540200	Weak transcription	K562	blood
33	chr2:48539400-48540400	Enhancers	Small Intestine	intestine
34	chr2:48539400-48540600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr2:48539400-48540600	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr2:48539400-48541000	Weak transcription	Stomach Mucosa	stomach

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