Variant report

Variant	rs12477141
Chromosome Location	chr2:55278845-55278846
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	TCF12	chr2:55277108-55278970	SK-N-SH	brain:	n/a	chr2:55277949-55277956 chr2:55278509-55278518
2	MAX	chr2:55277384-55278893	A549	lung:	n/a	chr2:55278420-55278430
3	TEAD4	chr2:55277123-55278992	K562	blood:	n/a	n/a
4	BCL3	chr2:55277282-55278900	A549	lung:	n/a	chr2:55277604-55277613 chr2:55277645-55277654 chr2:55278055-55278064
5	NR2F2	chr2:55277170-55278978	K562	blood:	n/a	n/a
6	POLR2A	chr2:55275602-55278945	HCT-116	colon:	n/a	n/a
7	RCOR1	chr2:55275614-55278876	Hela-S3	cervix:	n/a	n/a
8	BRCA1	chr2:55277481-55279097	Hela-S3	cervix:	n/a	chr2:55277795-55277802
9	SIN3AK20	chr2:55277897-55278908	A549	lung:	n/a	n/a
10	MAFK	chr2:55278216-55278984	Hela-S3	cervix:	n/a	chr2:55278509-55278518
11	MEF2A	chr2:55278137-55278869	SK-N-SH	brain:	n/a	chr2:55278139-55278154
12	TEAD4	chr2:55278217-55278923	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr2:55275829-55278945	SK-N-MC	brain:	n/a	n/a
14	TCF12	chr2:55275501-55278974	A549	lung:	n/a	chr2:55277949-55277956 chr2:55275946-55275954 chr2:55278509-55278518
15	RXRA	chr2:55277975-55278933	SK-N-SH	brain:	n/a	chr2:55278024-55278044
16	MXI1	chr2:55275607-55278907	IMR90	lung:	n/a	n/a
17	MAX	chr2:55277085-55278950	A549	lung:	n/a	chr2:55278420-55278430
18	TEAD4	chr2:55277956-55278925	SK-N-SH	brain:	n/a	n/a
19	JUN	chr2:55275513-55278923	K562	blood:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55277702-55277711 chr2:55278401-55278411
20	JUND	chr2:55277096-55279068	SK-N-SH	brain:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55277700-55277711 chr2:55277702-55277711 chr2:55278401-55278411 chr2:55278400-55278411
21	POLR2A	chr2:55275591-55278852	K562	blood:	n/a	n/a
22	PBX3	chr2:55277251-55278860	SK-N-SH	brain:	n/a	chr2:55277751-55277760 chr2:55277777-55277797
23	POLR2A	chr2:55275124-55278891	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr2:55274966-55278956	Hela-S3	cervix:	n/a	n/a
25	USF1	chr2:55277866-55278865	A549	lung:	n/a	n/a
26	POLR2A	chr2:55277231-55278895	GM12891	blood:	n/a	n/a
27	NFIC	chr2:55277359-55278941	HepG2	liver:	n/a	n/a
28	CBX3	chr2:55278158-55279054	HCT-116	colon:	n/a	n/a
29	MXI1	chr2:55274609-55279166	SK-N-SH	brain:	n/a	n/a
30	CHD1	chr2:55271552-55280181	IMR90	lung:	n/a	chr2:55276840-55276850
31	SP1	chr2:55277097-55279066	A549	lung:	n/a	chr2:55277924-55277934 chr2:55277870-55277881 chr2:55277870-55277882 chr2:55277984-55277996 chr2:55277984-55277996 chr2:55277986-55277995 chr2:55277893-55277904 chr2:55277871-55277880 chr2:55277872-55277881 chr2:55277985-55277994 chr2:55278551-55278572 chr2:55277871-55277881 chr2:55277870-55277882
32	JUND	chr2:55277007-55278957	SK-N-SH	brain:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55277700-55277711 chr2:55277702-55277711 chr2:55278401-55278411 chr2:55278400-55278411
33	JUN	chr2:55278149-55278931	Hela-S3	cervix:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55278401-55278411
34	FOSL2	chr2:55277271-55278982	SK-N-SH	brain:	n/a	chr2:55277701-55277712 chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278401-55278412 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55277702-55277711 chr2:55278401-55278411
35	SIX5	chr2:55277142-55278846	A549	lung:	n/a	n/a
36	FOS	chr2:55278214-55280128	MCF10A-Er-Src	breast:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55279171-55279183 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55278506-55278517 chr2:55278401-55278411
37	CUX1	chr2:55278173-55278870	K562	blood:	n/a	chr2:55278556-55278570
38	EP300	chr2:55276941-55278912	ECC-1	luminal epithelium:	n/a	chr2:55277644-55277653
39	TEAD4	chr2:55278127-55278926	K562	blood:	n/a	n/a
40	STAT3	chr2:55278154-55278874	Hela-S3	cervix:	n/a	chr2:55278443-55278450
41	POLR2A	chr2:55275655-55278975	HUVEC	blood vessel:	n/a	n/a
42	NFIC	chr2:55277199-55278974	SK-N-SH	brain:	n/a	n/a
43	MAFK	chr2:55278310-55278848	HepG2	liver:	n/a	chr2:55278509-55278518
44	EP300	chr2:55278005-55278952	SK-N-SH	brain:	n/a	n/a
45	JUND	chr2:55277313-55278914	SK-N-SH	brain:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55277700-55277711 chr2:55277702-55277711 chr2:55278401-55278411 chr2:55278400-55278411
46	POLR2A	chr2:55277070-55278966	U87	brain:	n/a	n/a
47	POLR2A	chr2:55277088-55278865	U87	brain:	n/a	n/a
48	KAP1	chr2:55278101-55278852	HEK293	kidney:	n/a	n/a
49	ZKSCAN1	chr2:55276099-55278874	Hela-S3	cervix:	n/a	n/a
50	EP300	chr2:55278155-55278921	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55276798..55279791-chr2:55841794..55843892,2	K562	blood:
2	chr2:55278226..55280278-chr2:55389625..55391199,2	MCF-7	breast:
3	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
4	chr2:55278691..55279239-chr20:21284043..21284729,2	Hela-S3	cervix:
5	chr2:55275304..55279887-chr2:55458370..55461390,5	K562	blood:
6	chr2:55278214..55278967-chr2:88926117..88926888,2	Hela-S3	cervix:
7	chr2:55278333..55279964-chr2:55343174..55345064,2	MCF-7	breast:
8	chr2:55278606..55281085-chr2:55289009..55290511,2	K562	blood:
9	chr2:55276121..55279274-chr2:55457448..55460901,6	K562	blood:
10	chr2:55273237..55279836-chr2:55336432..55344363,17	K562	blood:
11	chr2:55278300..55281080-chr2:55325086..55327233,3	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000266376	Chromatin interaction
ENSG00000138041	Chromatin interaction
ENSG00000143947	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000088930	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10496037	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12465266	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12479310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1348528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17046647	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1822618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55762835	0.80[EUR][1000 genomes]
rs60825248	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55272400-55279600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:55273400-55279800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:55273800-55279000	Active TSS	Psoas Muscle	Psoas
4	chr2:55273800-55279200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:55274200-55279000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:55274200-55279200	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr2:55274200-55279600	Active TSS	HMEC	breast
8	chr2:55274600-55279200	Active TSS	NHEK	skin
9	chr2:55274800-55279000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr2:55274800-55279000	Active TSS	Right Ventricle	heart
11	chr2:55275000-55279400	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr2:55275000-55279400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:55275200-55279200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:55275400-55279000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:55275400-55279600	Active TSS	A549	lung
16	chr2:55275800-55279200	Active TSS	Thymus	Thymus
17	chr2:55275800-55280000	Active TSS	NHLF	lung
18	chr2:55276200-55279200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:55277400-55279000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:55277400-55279200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:55277800-55279000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:55277800-55279400	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr2:55277800-55279800	Active TSS	Right Atrium	heart
24	chr2:55278000-55279000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr2:55278000-55279000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr2:55278000-55279000	Flanking Active TSS	Osteobl	bone
27	chr2:55278000-55279400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr2:55278000-55279400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr2:55278000-55279600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr2:55278000-55280000	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr2:55278000-55280000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:55278000-55280200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:55278200-55279000	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr2:55278200-55279000	Flanking Active TSS	Fetal Lung	lung
35	chr2:55278200-55279000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr2:55278200-55279400	Flanking Active TSS	Fetal Kidney	kidney
37	chr2:55278200-55279400	Enhancers	Small Intestine	intestine
38	chr2:55278200-55279800	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr2:55278200-55279800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr2:55278200-55280000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr2:55278200-55280000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr2:55278200-55282600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:55278200-55288800	Weak transcription	Lung	lung
44	chr2:55278400-55279000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr2:55278400-55279000	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr2:55278400-55279000	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr2:55278400-55279000	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr2:55278400-55279000	Flanking Active TSS	Fetal Intestine Small	intestine
49	chr2:55278400-55279000	Flanking Active TSS	Fetal Muscle Leg	muscle
50	chr2:55278400-55279000	Flanking Active TSS	Fetal Stomach	stomach

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