Variant report

Variant	rs4290706
Chromosome Location	chr2:48541044-48541045
allele	A/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	TAF1	chr2:48540991-48542028	A549	lung:	n/a	n/a
2	POLR2A	chr2:48540939-48543359	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:48540878-48543216	SK-N-MC	brain:	n/a	n/a
4	MAX	chr2:48540993-48543438	SK-N-SH	brain:	n/a	chr2:48543161-48543171 chr2:48543159-48543172 chr2:48542391-48542401 chr2:48543160-48543170 chr2:48541745-48541754 chr2:48543160-48543171 chr2:48541678-48541688 chr2:48542054-48542063 chr2:48543160-48543171 chr2:48543161-48543170 chr2:48543160-48543171 chr2:48543161-48543171 chr2:48543160-48543170
5	JUN	chr2:48540999-48542087	K562	blood:	n/a	chr2:48541697-48541706
6	MYC	chr2:48541025-48543644	A549	lung:	n/a	chr2:48543161-48543171 chr2:48543159-48543172 chr2:48542391-48542401 chr2:48543160-48543170 chr2:48541745-48541754 chr2:48543160-48543171 chr2:48541678-48541688 chr2:48542054-48542063 chr2:48543160-48543171 chr2:48543161-48543170 chr2:48543160-48543171 chr2:48543161-48543171 chr2:48543160-48543170
7	POLR2A	chr2:48541026-48543274	MCF-7	breast:	n/a	n/a
8	SMC3	chr2:48540684-48542019	GM12878	blood:	n/a	chr2:48541837-48541845
9	MXI1	chr2:48540999-48543726	IMR90	lung:	n/a	chr2:48541743-48541758 chr2:48543162-48543171 chr2:48543160-48543169 chr2:48543162-48543171
10	RCOR1	chr2:48540730-48543576	GM12878	blood:	n/a	n/a
11	MYBL2	chr2:48540845-48542020	HepG2	liver:	n/a	n/a
12	PML	chr2:48540962-48541586	K562	blood:	n/a	n/a
13	ATF2	chr2:48540729-48541627	GM12878	blood:	n/a	n/a
14	TAF1	chr2:48541025-48542297	K562	blood:	n/a	n/a
15	POLR2A	chr2:48541040-48541492	GM12891	blood:	n/a	n/a
16	NFIC	chr2:48540637-48541758	GM12878	blood:	n/a	n/a
17	SP1	chr2:48541000-48541934	HepG2	liver:	n/a	chr2:48541694-48541708 chr2:48541385-48541397 chr2:48541386-48541395 chr2:48541387-48541396 chr2:48541556-48541568 chr2:48541386-48541396 chr2:48541557-48541566 chr2:48541715-48541727 chr2:48541386-48541396 chr2:48541717-48541726 chr2:48541716-48541726 chr2:48541386-48541395 chr2:48541715-48541727 chr2:48541627-48541639 chr2:48541385-48541397 chr2:48541556-48541568
18	FOSL2	chr2:48540998-48541631	A549	lung:	n/a	n/a
19	POLR2A	chr2:48540107-48543489	GM12891	blood:	n/a	n/a
20	POLR2A	chr2:48540301-48543417	GM18951	blood:	n/a	n/a
21	POLR2A	chr2:48541024-48542095	HCT-116	colon:	n/a	n/a
22	MAZ	chr2:48541005-48543473	IMR90	lung:	n/a	chr2:48543161-48543171 chr2:48543159-48543172 chr2:48542391-48542401 chr2:48543160-48543170 chr2:48541745-48541754 chr2:48543160-48543171 chr2:48541678-48541688 chr2:48542054-48542063 chr2:48543160-48543171 chr2:48543161-48543170 chr2:48543160-48543171 chr2:48543161-48543171 chr2:48543160-48543170
23	NFIC	chr2:48541010-48542104	HepG2	liver:	n/a	n/a
24	RELA	chr2:48540295-48543281	GM15510	blood:	n/a	n/a
25	POLR2A	chr2:48540948-48543446	GM12892	blood:	n/a	n/a
26	POLR2A	chr2:48541009-48541612	GM12891	blood:	n/a	n/a
27	POLR2A	chr2:48541015-48543060	PANC-1	pancreas:	n/a	n/a
28	CBX3	chr2:48541025-48542015	HCT-116	colon:	n/a	n/a
29	POLR2A	chr2:48540308-48543338	K562	blood:	n/a	n/a
30	BCLAF1	chr2:48541027-48542258	GM12878	blood:	n/a	chr2:48541528-48541536 chr2:48542004-48542017 chr2:48542023-48542032 chr2:48541430-48541439 chr2:48542061-48542070 chr2:48541387-48541400
31	MAX	chr2:48540912-48543606	HepG2	liver:	n/a	chr2:48543161-48543171 chr2:48543159-48543172 chr2:48542391-48542401 chr2:48543160-48543170 chr2:48541745-48541754 chr2:48543160-48543171 chr2:48541678-48541688 chr2:48542054-48542063 chr2:48543160-48543171 chr2:48543161-48543170 chr2:48543160-48543171 chr2:48543161-48543171 chr2:48543160-48543170
32	POLR2A	chr2:48540282-48543461	Raji	blood:	n/a	n/a
33	TBL1XR1	chr2:48540725-48542358	GM12878	blood:	n/a	n/a
34	POLR2A	chr2:48541014-48543496	HL-60	blood:	n/a	n/a
35	POLR2A	chr2:48540239-48543382	GM12892	blood:	n/a	n/a
36	TEAD4	chr2:48540939-48541725	HepG2	liver:	n/a	n/a
37	POLR2A	chr2:48541019-48541991	SK-N-MC	brain:	n/a	n/a
38	POLR2A	chr2:48540673-48543277	PBDE	blood:	n/a	n/a
39	CTCF	chr2:48540661-48543738	A549	lung:	n/a	chr2:48541659-48541672 chr2:48542391-48542404 chr2:48541998-48542011
40	STAT5A	chr2:48541017-48541786	K562	blood:	n/a	n/a
41	MAX	chr2:48541011-48543528	ECC-1	luminal epithelium:	n/a	chr2:48543161-48543171 chr2:48543159-48543172 chr2:48542391-48542401 chr2:48543160-48543170 chr2:48541745-48541754 chr2:48543160-48543171 chr2:48541678-48541688 chr2:48542054-48542063 chr2:48543160-48543171 chr2:48543161-48543170 chr2:48543160-48543171 chr2:48543161-48543171 chr2:48543160-48543170
42	FOXM1	chr2:48540614-48542004	GM12878	blood:	n/a	n/a
43	BHLHE40	chr2:48540988-48543349	GM12878	blood:	n/a	chr2:48541996-48542012 chr2:48541814-48541830 chr2:48542765-48542781 chr2:48541804-48541820
44	EGR1	chr2:48540994-48542742	HCT-116	colon:	n/a	chr2:48542546-48542556 chr2:48542645-48542654 chr2:48542502-48542512 chr2:48541386-48541396 chr2:48541389-48541398 chr2:48541387-48541401 chr2:48541578-48541592 chr2:48541388-48541401 chr2:48541426-48541439 chr2:48542126-48542135 chr2:48542118-48542127 chr2:48541581-48541594 chr2:48542495-48542509 chr2:48541388-48541398 chr2:48542494-48542507 chr2:48542062-48542076 chr2:48541388-48541401 chr2:48542061-48542074 chr2:48541388-48541401 chr2:48541389-48541399 chr2:48541388-48541401 chr2:48542387-48542402 chr2:48541387-48541402
45	POLR2A	chr2:48540171-48543452	GM12878	blood:	n/a	n/a
46	BRCA1	chr2:48540950-48541922	Hela-S3	cervix:	n/a	n/a
47	MYC	chr2:48540941-48541663	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr2:48540974-48542066	PANC-1	pancreas:	n/a	n/a
49	POLR2A	chr2:48540139-48543407	GM15510	blood:	n/a	n/a
50	MAX	chr2:48540768-48543496	GM12878	blood:	n/a	chr2:48543161-48543171 chr2:48543159-48543172 chr2:48542391-48542401 chr2:48543160-48543170 chr2:48541745-48541754 chr2:48543160-48543171 chr2:48541678-48541688 chr2:48542054-48542063 chr2:48543160-48543171 chr2:48543161-48543170 chr2:48543160-48543171 chr2:48543161-48543171 chr2:48543160-48543170

No.	Distal block	Cell Line	Cell type
1	chr2:48541013..48541633-chr2:172864371..172865206,2	HCT-116	colon:
2	chr2:48539557..48542081-chr2:48666297..48668955,4	MCF-7	breast:
3	chr2:48515255..48518583-chr2:48539283..48541492,3	K562	blood:
4	chr2:48133540..48135075-chr2:48540885..48543276,2	K562	blood:
5	chr2:48492280..48493854-chr2:48539785..48541732,2	K562	blood:
6	chr2:48532704..48536258-chr2:48538581..48541257,5	K562	blood:
7	chr2:48540805..48543133-chr2:48691336..48694309,2	K562	blood:
8	chr2:48540677..48543829-chr2:48665802..48669252,3	K562	blood:

Variant related genes	Relation type
FOXN2	TF binding region
ENSG00000162869	Chromatin interaction
ENSG00000233230	Chromatin interaction
ENSG00000272663	Chromatin interaction
ENSG00000115840	Chromatin interaction
ENSG00000172878	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	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10180295	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10186237	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10193072	0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10199431	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10208124	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11676168	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11682044	0.82[AFR][1000 genomes];0.98[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	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13385535	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13386751	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13387171	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13388291	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13392004	0.83[EUR][1000 genomes]
rs13426834	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13432998	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2471405	0.85[ASN][1000 genomes]
rs28806843	0.81[AFR][1000 genomes];0.94[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]
rs4344965	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4411759	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4547573	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4641990	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs56352447	0.94[ASN][1000 genomes]
rs57668696	0.94[AFR][1000 genomes];0.85[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	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62137003	0.85[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	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62138801	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545027	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545028	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545029	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545030	0.92[AFR][1000 genomes];0.85[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	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6712029	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6743757	0.82[EUR][1000 genomes]
rs6757206	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72818493	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72820405	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72887649	0.96[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	0.86[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	0.86[AFR][1000 genomes];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:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48538800-48541200	Enhancers	NHEK	skin
2	chr2:48540200-48541200	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr2:48540200-48541400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr2:48540200-48541400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr2:48540200-48541400	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr2:48540200-48541400	Flanking Active TSS	Dnd41	blood
7	chr2:48540200-48541400	Flanking Active TSS	K562	blood
8	chr2:48540200-48542800	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr2:48540200-48543000	Active TSS	Thymus	Thymus
10	chr2:48540400-48541200	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr2:48540400-48541200	Flanking Active TSS	HepG2	liver
12	chr2:48540400-48541400	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr2:48540400-48541800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:48540400-48541800	Weak transcription	Small Intestine	intestine
15	chr2:48540600-48541200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:48540600-48541200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr2:48540600-48541200	Active TSS	Right Atrium	heart
18	chr2:48540600-48541200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:48540600-48541400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr2:48540600-48541400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:48540600-48542800	Active TSS	Rectal Smooth Muscle	rectum
22	chr2:48540600-48542800	Active TSS	Stomach Smooth Muscle	stomach
23	chr2:48540600-48542800	Active TSS	Osteobl	bone
24	chr2:48540600-48543400	Active TSS	Aorta	Aorta
25	chr2:48540600-48543400	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr2:48540600-48543400	Active TSS	Psoas Muscle	Psoas
27	chr2:48540600-48543600	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr2:48540600-48543600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:48540600-48544000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:48540600-48544200	Active TSS	Brain Angular Gyrus	brain
31	chr2:48540600-48544600	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr2:48540600-48547400	Active TSS	GM12878-XiMat	blood
33	chr2:48540800-48541200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr2:48540800-48541200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:48540800-48541400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr2:48540800-48541400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:48540800-48541400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:48540800-48541400	Flanking Active TSS	Liver	Liver
39	chr2:48540800-48541400	Flanking Active TSS	HUVEC	blood vessel
40	chr2:48540800-48542400	Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr2:48540800-48542600	Active TSS	Primary T cells fromperipheralblood	blood
42	chr2:48540800-48542800	Active TSS	Fetal Thymus	thymus
43	chr2:48540800-48543000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:48540800-48543000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr2:48540800-48543000	Active TSS	Duodenum Mucosa	Duodenum
46	chr2:48540800-48543000	Active TSS	Placenta	Placenta
47	chr2:48540800-48543200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:48540800-48543200	Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr2:48540800-48543200	Active TSS	Fetal Lung	lung
50	chr2:48540800-48543400	Active TSS	HUES64 Cell Line	embryonic stem cell

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