Variant report

Variant	rs72818494
Chromosome Location	chr2:48540314-48540315
allele	C/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	POLR2A	chr2:48540107-48543489	GM12891	blood:	n/a	n/a
2	POLR2A	chr2:48540301-48543417	GM18951	blood:	n/a	n/a
3	RELA	chr2:48540295-48543281	GM15510	blood:	n/a	n/a
4	POLR2A	chr2:48540308-48543338	K562	blood:	n/a	n/a
5	POLR2A	chr2:48540282-48543461	Raji	blood:	n/a	n/a
6	POLR2A	chr2:48540239-48543382	GM12892	blood:	n/a	n/a
7	POLR2A	chr2:48540171-48543452	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:48540139-48543407	GM15510	blood:	n/a	n/a
9	RELA	chr2:48540241-48543316	GM19099	blood:	n/a	n/a
10	TBP	chr2:48540285-48543395	K562	blood:	n/a	n/a
11	MAX	chr2:48540174-48540486	K562	blood:	n/a	n/a
12	POLR2A	chr2:48540232-48543419	GM18505	blood:	n/a	n/a
13	HEY1	chr2:48540113-48543427	HepG2	liver:	n/a	chr2:48542008-48542023 chr2:48542497-48542512 chr2:48541386-48541401
14	POLR2A	chr2:48540299-48543355	GM12878	blood:	n/a	n/a
15	JUN	chr2:48539938-48543624	K562	blood:	n/a	chr2:48540933-48540945 chr2:48541697-48541706
16	POLR2A	chr2:48540208-48543378	GM19193	blood:	n/a	n/a
17	POLR2A	chr2:48540189-48543229	K562	blood:	n/a	n/a
18	POLR2A	chr2:48540286-48542986	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr2:48540239-48540713	K562	blood:	n/a	n/a
20	POLR2A	chr2:48540173-48543478	GM19099	blood:	n/a	n/a
21	WRNIP1	chr2:48540209-48540409	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:48540257-48543368	GM18526	blood:	n/a	n/a
23	POLR2A	chr2:48539070-48543442	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr2:48540305-48543433	GM12878	blood:	n/a	n/a
25	RELA	chr2:48540241-48543442	GM12891	blood:	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: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10495952	0.87[AMR][1000 genomes]
rs11676036	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11678403	0.82[ASN][1000 genomes]
rs11679523	0.83[ASN][1000 genomes]
rs11680916	0.83[ASN][1000 genomes]
rs11681409	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11682633	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11684517	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11685861	0.84[ASN][1000 genomes]
rs11686007	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11687708	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11688481	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11690690	0.83[ASN][1000 genomes]
rs11690748	0.82[ASN][1000 genomes]
rs11690845	0.83[ASN][1000 genomes]
rs17037289	0.80[ASN][1000 genomes]
rs17855177	0.83[ASN][1000 genomes]
rs4344965	0.82[ASN][1000 genomes]
rs55660911	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs55761545	0.90[ASN][1000 genomes]
rs55788229	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57131168	0.98[ASN][1000 genomes]
rs57537506	0.84[ASN][1000 genomes]
rs57893565	0.82[ASN][1000 genomes]
rs58012056	0.84[ASN][1000 genomes]
rs59697023	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60815228	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62137015	0.82[ASN][1000 genomes]
rs6705802	0.83[ASN][1000 genomes]
rs6718068	0.83[ASN][1000 genomes]
rs6722246	0.83[ASN][1000 genomes]
rs6743757	0.82[ASN][1000 genomes]
rs6745580	0.84[ASN][1000 genomes]
rs6756596	0.81[ASN][1000 genomes]
rs72818478	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72818488	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72818491	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72818502	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72820403	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72820404	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72820409	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72820411	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72820415	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72820416	0.86[ASN][1000 genomes]
rs72820418	0.83[ASN][1000 genomes]
rs72820420	0.84[ASN][1000 genomes]
rs72820422	0.85[ASN][1000 genomes]
rs72820423	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72820424	0.81[ASN][1000 genomes]
rs72820427	0.81[ASN][1000 genomes]
rs72820433	0.87[AMR][1000 genomes]
rs72820436	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72820437	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72820439	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72820445	0.83[ASN][1000 genomes]
rs7562069	0.83[ASN][1000 genomes]
rs7566239	0.82[ASN][1000 genomes]
rs7573316	0.83[ASN][1000 genomes]
rs7576964	0.83[ASN][1000 genomes]
rs7577237	0.84[ASN][1000 genomes]
rs7579932	0.83[ASN][1000 genomes]
rs7606104	0.84[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:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48535600-48540400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:48538400-48540400	Enhancers	HepG2	liver
3	chr2:48538400-48540600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:48538600-48540400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:48538600-48540800	Enhancers	Fetal Intestine Large	intestine
6	chr2:48538800-48541200	Enhancers	NHEK	skin
7	chr2:48539000-48540400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:48539000-48541000	Enhancers	Fetal Intestine Small	intestine
9	chr2:48539200-48541000	Enhancers	HMEC	breast
10	chr2:48539400-48540400	Enhancers	Small Intestine	intestine
11	chr2:48539400-48540600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr2:48539400-48540600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr2:48539400-48541000	Weak transcription	Stomach Mucosa	stomach
14	chr2:48539600-48540400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:48539600-48540400	Enhancers	Primary T cells fromperipheralblood	blood
16	chr2:48539600-48540400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:48539600-48540600	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr2:48539600-48540800	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr2:48539600-48541000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr2:48539800-48540400	Enhancers	Primary B cells from cord blood	blood
21	chr2:48539800-48540600	Enhancers	Psoas Muscle	Psoas
22	chr2:48539800-48540800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:48539800-48541000	Weak transcription	Hela-S3	cervix
24	chr2:48540200-48540400	Enhancers	Primary B cells from peripheral blood	blood
25	chr2:48540200-48540400	Enhancers	Primary hematopoietic stem cells	blood
26	chr2:48540200-48540400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr2:48540200-48540400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:48540200-48540400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:48540200-48540400	Flanking Active TSS	Liver	Liver
30	chr2:48540200-48540400	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr2:48540200-48540400	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr2:48540200-48540400	Enhancers	Placenta Amnion	Placenta Amnion
33	chr2:48540200-48540400	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr2:48540200-48540400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr2:48540200-48540600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:48540200-48540600	Flanking Active TSS	GM12878-XiMat	blood
37	chr2:48540200-48540600	Enhancers	NHLF	lung
38	chr2:48540200-48540800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:48540200-48540800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr2:48540200-48540800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr2:48540200-48540800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:48540200-48540800	Enhancers	Fetal Muscle Leg	muscle
43	chr2:48540200-48540800	Enhancers	Placenta	Placenta
44	chr2:48540200-48540800	Enhancers	Fetal Thymus	thymus
45	chr2:48540200-48540800	Enhancers	NHDF-Ad	bronchial
46	chr2:48540200-48541000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:48540200-48541000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr2:48540200-48541000	Enhancers	Colonic Mucosa	Colon
49	chr2:48540200-48541000	Enhancers	Fetal Heart	heart
50	chr2:48540200-48541000	Enhancers	Pancreas	Pancrea

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