Variant report

Variant	rs6545469
Chromosome Location	chr2:55277858-55277859
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	ATF1	chr2:55277375-55278083	K562	blood:	n/a	n/a
2	POU2F2	chr2:55277304-55278009	GM12891	blood:	n/a	n/a
3	POLR2A	chr2:55277249-55278095	GM10847	blood:	n/a	n/a
4	TCF12	chr2:55277108-55278970	SK-N-SH	brain:	n/a	chr2:55277949-55277956 chr2:55278509-55278518
5	RCOR1	chr2:55277262-55278065	K562	blood:	n/a	n/a
6	BRCA1	chr2:55277497-55278038	GM12878	blood:	n/a	chr2:55277795-55277802
7	SPI1	chr2:55277641-55278222	GM12891	blood:	n/a	chr2:55278119-55278132 chr2:55278055-55278064 chr2:55277835-55277848 chr2:55277838-55277845 chr2:55277718-55277731 chr2:55277836-55277849
8	MAFK	chr2:55277335-55277999	Hela-S3	cervix:	n/a	chr2:55277832-55277847
9	CREB1	chr2:55277249-55278150	H1-hESC	embryonic stem cell:	n/a	n/a
10	SPI1	chr2:55277625-55277958	K562	blood:	n/a	chr2:55277835-55277848 chr2:55277838-55277845 chr2:55277718-55277731 chr2:55277836-55277849
11	ELF1	chr2:55277212-55278171	HepG2	liver:	n/a	chr2:55277646-55277655
12	MAX	chr2:55277243-55277925	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr2:55277384-55278893	A549	lung:	n/a	chr2:55278420-55278430
14	NFIC	chr2:55277437-55277972	GM12878	blood:	n/a	n/a
15	POLR2A	chr2:55275630-55278124	H1-neurons	neurons:	n/a	n/a
16	TEAD4	chr2:55277123-55278992	K562	blood:	n/a	n/a
17	TAF1	chr2:55277170-55278561	K562	blood:	n/a	n/a
18	GABPA	chr2:55277388-55278643	MCF-7	breast:	n/a	n/a
19	POLR2A	chr2:55277814-55278180	HepG2	liver:	n/a	n/a
20	BCL3	chr2:55277282-55278900	A549	lung:	n/a	chr2:55277604-55277613 chr2:55277645-55277654 chr2:55278055-55278064
21	POLR2A	chr2:55275958-55278821	HUVEC	blood vessel:	n/a	n/a
22	FOS	chr2:55277531-55278002	MCF10A-Er-Src	breast:	n/a	chr2:55277702-55277711
23	UBTF	chr2:55274752-55278735	K562	blood:	n/a	n/a
24	SMARCC1	chr2:55277068-55278785	Hela-S3	cervix:	n/a	chr2:55278402-55278411 chr2:55277702-55277711
25	TAF1	chr2:55277135-55277959	H1-neurons	neurons:	n/a	n/a
26	POLR2A	chr2:55276021-55278144	GM12892	blood:	n/a	n/a
27	FOSL1	chr2:55277458-55277863	K562	blood:	n/a	chr2:55277700-55277711 chr2:55277702-55277711
28	POLR2A	chr2:55277116-55278826	PBDE	blood:	n/a	n/a
29	HA-E2F1	chr2:55276534-55278194	Hela-S3	cervix:	n/a	chr2:55277644-55277654 chr2:55277750-55277759 chr2:55277985-55277994
30	POLR2A	chr2:55276933-55278685	K562	blood:	n/a	n/a
31	NR2F2	chr2:55277170-55278978	K562	blood:	n/a	n/a
32	IRF3	chr2:55277588-55277941	Hela-S3	cervix:	n/a	chr2:55277870-55277884
33	POLR2A	chr2:55275602-55278945	HCT-116	colon:	n/a	n/a
34	FOSL2	chr2:55277277-55277985	MCF-7	breast:	n/a	chr2:55277701-55277712 chr2:55277702-55277711
35	CEBPB	chr2:55277772-55277954	HepG2	liver:	n/a	n/a
36	SIN3A	chr2:55275650-55278654	H1-hESC	embryonic stem cell:	n/a	chr2:55276189-55276200
37	RCOR1	chr2:55275614-55278876	Hela-S3	cervix:	n/a	n/a
38	GABPA	chr2:55277321-55278549	MCF-7	breast:	n/a	n/a
39	BRCA1	chr2:55277481-55279097	Hela-S3	cervix:	n/a	chr2:55277795-55277802
40	POLR2A	chr2:55277242-55278783	HUVEC	blood vessel:	n/a	n/a
41	CHD1	chr2:55277259-55278517	GM12878	blood:	n/a	n/a
42	REST	chr2:55277118-55277903	H1-neurons	neurons:	n/a	n/a
43	RELA	chr2:55277268-55278071	GM12892	blood:	n/a	n/a
44	FOS	chr2:55277607-55277989	GM12878	blood:	n/a	chr2:55277702-55277711
45	SRF	chr2:55277474-55277942	GM12878	blood:	n/a	n/a
46	RUNX3	chr2:55277173-55278605	GM12878	blood:	n/a	chr2:55278265-55278280
47	POLR2A	chr2:55277032-55278781	PANC-1	pancreas:	n/a	n/a
48	JUND	chr2:55275956-55278211	A549	lung:	n/a	chr2:55277700-55277711 chr2:55277702-55277711
49	MTA3	chr2:55277082-55278821	GM12878	blood:	n/a	n/a
50	POLR2A	chr2:55275648-55278177	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55276798..55279791-chr2:55841794..55843892,2	K562	blood:
2	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
3	chr2:55277189..55278043-chr8:101733959..101734464,2	HCT-116	colon:
4	chr2:55241176..55242945-chr2:55276344..55278140,2	MCF-7	breast:
5	chr1:36235207..36235805-chr2:55277148..55277958,2	Hela-S3	cervix:
6	chr2:55275304..55279887-chr2:55458370..55461390,5	K562	blood:
7	chr2:55276121..55279274-chr2:55457448..55460901,6	K562	blood:
8	chr2:55277102..55277934-chr7:75156921..75157592,2	Hela-S3	cervix:
9	chr2:55273237..55279836-chr2:55336432..55344363,17	K562	blood:
10	chr2:55276251..55278794-chr2:55450594..55452106,2	MCF-7	breast:
11	chr2:55277528..55278356-chr7:129844697..129845281,2	NB4	blood:
12	chr16:284775..285377-chr2:55277111..55278067,2	Hela-S3	cervix:
13	chr10:76871028..76871837-chr2:55277241..55278117,2	Hela-S3	cervix:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000156671	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000200086	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000092853	Chromatin interaction
ENSG00000138041	Chromatin interaction
ENSG00000146842	Chromatin interaction
ENSG00000266376	Chromatin interaction
ENSG00000143947	Chromatin interaction
ENSG00000127957	Chromatin interaction
ENSG00000070756	Chromatin interaction
ENSG00000167930	Chromatin interaction
ENSG00000227799	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10170102	0.81[EUR][1000 genomes]
rs10174447	0.85[AFR][1000 genomes]
rs10175952	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10180207	0.80[EUR][1000 genomes]
rs10181115	0.81[EUR][1000 genomes]
rs10182203	0.86[EUR][1000 genomes]
rs10191748	0.84[AMR][1000 genomes]
rs10191774	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10197533	0.84[ASW][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10197591	1.00[CEU][hapmap]
rs10206953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10207701	0.87[AMR][1000 genomes]
rs11125554	0.86[EUR][1000 genomes]
rs13387710	0.87[AMR][1000 genomes]
rs13387836	0.81[AFR][1000 genomes]
rs13400353	1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13401780	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs13416852	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17046569	0.84[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs28485107	0.85[AFR][1000 genomes]
rs4358163	0.82[MEX][hapmap];0.82[TSI][hapmap]
rs6545470	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6715980	0.84[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs6744637	0.84[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.98[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6758258	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap]
rs6760773	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72912579	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7584992	1.00[MEX][hapmap]
rs7592869	1.00[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55271400-55278200	Active TSS	HSMMtube	muscle
2	chr2:55272400-55279600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:55273200-55278400	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr2:55273200-55278400	Active TSS	GM12878-XiMat	blood
5	chr2:55273400-55279800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr2:55273800-55278600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr2:55273800-55278600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:55273800-55279000	Active TSS	Psoas Muscle	Psoas
9	chr2:55273800-55279200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:55274000-55278200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:55274000-55278200	Active TSS	NH-A	brain
12	chr2:55274200-55278400	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr2:55274200-55278600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:55274200-55278600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:55274200-55279000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:55274200-55279200	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr2:55274200-55279600	Active TSS	HMEC	breast
18	chr2:55274400-55278800	Active TSS	Fetal Brain Male	brain
19	chr2:55274600-55278000	Active TSS	Osteobl	bone
20	chr2:55274600-55278400	Active TSS	Fetal Muscle Leg	muscle
21	chr2:55274600-55278400	Active TSS	Fetal Stomach	stomach
22	chr2:55274600-55278600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:55274600-55278600	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr2:55274600-55278800	Active TSS	Aorta	Aorta
25	chr2:55274600-55278800	Active TSS	Fetal Muscle Trunk	muscle
26	chr2:55274600-55279200	Active TSS	NHEK	skin
27	chr2:55274800-55278200	Active TSS	Fetal Intestine Large	intestine
28	chr2:55274800-55278400	Active TSS	Colon Smooth Muscle	Colon
29	chr2:55274800-55278400	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr2:55274800-55278600	Active TSS	Hela-S3	cervix
31	chr2:55274800-55278800	Active TSS	Ovary	ovary
32	chr2:55274800-55279000	Active TSS	H9 Cell Line	embryonic stem cell
33	chr2:55274800-55279000	Active TSS	Right Ventricle	heart
34	chr2:55275000-55278000	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr2:55275000-55278200	Active TSS	Brain Angular Gyrus	brain
36	chr2:55275000-55278200	Active TSS	Lung	lung
37	chr2:55275000-55278400	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr2:55275000-55278400	Active TSS	Stomach Smooth Muscle	stomach
39	chr2:55275000-55278600	Active TSS	Colonic Mucosa	Colon
40	chr2:55275000-55278800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr2:55275000-55278800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr2:55275000-55279400	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr2:55275000-55279400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:55275200-55278200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:55275200-55278400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:55275200-55278400	Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr2:55275200-55278400	Active TSS	Brain Substantia Nigra	brain
48	chr2:55275200-55278600	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr2:55275200-55278600	Active TSS	Placenta Amnion	Placenta Amnion
50	chr2:55275200-55278600	Active TSS	Stomach Mucosa	stomach

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