Variant report

Variant	rs72887649
Chromosome Location	chr2:48539974-48539975
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	JUN	chr2:48539938-48543624	K562	blood:	n/a	chr2:48540933-48540945 chr2:48541697-48541706
2	POLR2A	chr2:48539070-48543442	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	chr2:48492280..48493854-chr2:48539785..48541732,2	K562	blood:
5	chr2:48532704..48536258-chr2:48538581..48541257,5	K562	blood:

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

Extended variants
information (count: 69 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10153773	0.85[ASN][1000 genomes]
rs10174717	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10180295	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10186237	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10193072	0.98[ASN][1000 genomes]
rs10199431	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10208124	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11676168	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11682044	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685861	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11690690	0.82[AMR][1000 genomes]
rs12616792	0.87[ASN][1000 genomes]
rs12713008	0.87[ASN][1000 genomes]
rs12713009	0.87[ASN][1000 genomes]
rs13383364	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13385535	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13386751	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13387171	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13388291	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13426834	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13432998	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2471405	0.85[ASN][1000 genomes]
rs28806843	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28841370	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4290706	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4344965	0.81[AMR][1000 genomes]
rs4411759	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4547573	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4641990	0.90[ASN][1000 genomes]
rs56352447	0.94[ASN][1000 genomes]
rs57668696	0.83[AMR][1000 genomes];0.87[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	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60677957	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62136987	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62137001	0.89[ASN][1000 genomes]
rs62137002	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62137003	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[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[AMR][1000 genomes]
rs62138801	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545027	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545028	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545029	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545030	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545034	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545035	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545036	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6712029	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6757206	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72818493	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72820405	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7340322	0.88[ASN][1000 genomes]
rs7568960	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7574125	0.83[ASN][1000 genomes]
rs7579932	0.83[AMR][1000 genomes]
rs7600794	0.82[AMR][1000 genomes]
rs7606104	0.82[AMR][1000 genomes]
rs9309152	0.82[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:44 , 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	chr2:48534400-48540200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:48534600-48540200	Weak transcription	Adipose Nuclei	Adipose
4	chr2:48534600-48540200	Weak transcription	NHDF-Ad	bronchial
5	chr2:48535600-48540400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:48538400-48540400	Enhancers	HepG2	liver
7	chr2:48538400-48540600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:48538600-48540400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr2:48538600-48540800	Enhancers	Fetal Intestine Large	intestine
10	chr2:48538800-48540200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:48538800-48541200	Enhancers	NHEK	skin
12	chr2:48539000-48540200	Enhancers	Liver	Liver
13	chr2:48539000-48540400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:48539000-48541000	Enhancers	Fetal Intestine Small	intestine
15	chr2:48539200-48540000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:48539200-48540200	Enhancers	Primary T cells from cord blood	blood
17	chr2:48539200-48540200	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr2:48539200-48540200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:48539200-48540200	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr2:48539200-48540200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr2:48539200-48541000	Enhancers	HMEC	breast
22	chr2:48539400-48540200	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr2:48539400-48540200	Enhancers	Duodenum Mucosa	Duodenum
24	chr2:48539400-48540200	Weak transcription	K562	blood
25	chr2:48539400-48540400	Enhancers	Small Intestine	intestine
26	chr2:48539400-48540600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr2:48539400-48540600	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr2:48539400-48541000	Weak transcription	Stomach Mucosa	stomach
29	chr2:48539600-48540200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr2:48539600-48540200	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr2:48539600-48540200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr2:48539600-48540400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr2:48539600-48540400	Enhancers	Primary T cells fromperipheralblood	blood
34	chr2:48539600-48540400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:48539600-48540600	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr2:48539600-48540800	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr2:48539600-48541000	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr2:48539800-48540000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr2:48539800-48540000	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr2:48539800-48540200	Weak transcription	Placenta	Placenta
41	chr2:48539800-48540400	Enhancers	Primary B cells from cord blood	blood
42	chr2:48539800-48540600	Enhancers	Psoas Muscle	Psoas
43	chr2:48539800-48540800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:48539800-48541000	Weak transcription	Hela-S3	cervix

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