Variant report

Variant	rs3002293
Chromosome Location	chr1:150980552-150980553
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	GATA3	chr1:150980477-150980830	MCF-7	breast:	n/a	chr1:150980550-150980559
2	SIN3AK20	chr1:150980180-150981912	MCF-7	breast:	n/a	n/a
3	HEY1	chr1:150980525-150980890	HepG2	liver:	n/a	n/a
4	YY1	chr1:150980534-150981184	GM12878	blood:	n/a	chr1:150980883-150980892
5	TAL1	chr1:150980518-150981149	K562	blood:	n/a	chr1:150980623-150980638
6	GTF3C2	chr1:150980434-150981592	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:150980409-150981886	HepG2	liver:	n/a	n/a
8	HCFC1	chr1:150980547-150981190	K562	blood:	n/a	n/a
9	ARID3A	chr1:150980552-150980811	K562	blood:	n/a	n/a
10	SP1	chr1:150980364-150981118	HepG2	liver:	n/a	chr1:150980878-150980890 chr1:150980825-150980835 chr1:150980880-150980889 chr1:150980825-150980835 chr1:150980824-150980836 chr1:150980878-150980890 chr1:150980879-150980888 chr1:150980824-150980836
11	NR2F2	chr1:150980335-150981268	K562	blood:	n/a	n/a
12	MAX	chr1:150980509-150981176	HepG2	liver:	n/a	chr1:150980818-150980827
13	TBL1XR1	chr1:150980324-150981564	K562	blood:	n/a	n/a
14	GTF2F1	chr1:150980469-150981229	K562	blood:	n/a	n/a
15	POLR2A	chr1:150980501-150981302	PANC-1	pancreas:	n/a	n/a
16	REST	chr1:150980530-150981339	A549	lung:	n/a	n/a
17	BRCA1	chr1:150980531-150980950	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr1:150980416-150981866	MCF-7	breast:	n/a	chr1:150980818-150980827
19	MAX	chr1:150980468-150981748	A549	lung:	n/a	chr1:150980818-150980827
20	GATA3	chr1:150980425-150980760	MCF-7	breast:	n/a	chr1:150980550-150980559
21	ZNF217	chr1:150980465-150980877	MCF-7	breast:	n/a	n/a
22	GTF2B	chr1:150980544-150981047	K562	blood:	n/a	n/a
23	ZC3H11A	chr1:150980448-150981159	K562	blood:	n/a	n/a
24	POLR2A	chr1:150980485-150981505	PBDE	blood:	n/a	n/a
25	SP1	chr1:150980522-150981086	H1-hESC	embryonic stem cell:	n/a	chr1:150980878-150980890 chr1:150980825-150980835 chr1:150980880-150980889 chr1:150980825-150980835 chr1:150980824-150980836 chr1:150980878-150980890 chr1:150980879-150980888 chr1:150980824-150980836
26	EP300	chr1:150980106-150981033	HepG2	liver:	n/a	n/a
27	HCFC1	chr1:150980019-150982095	Hela-S3	cervix:	n/a	n/a
28	GABPA	chr1:150980256-150981937	MCF-7	breast:	n/a	n/a
29	CREB1	chr1:150980514-150981506	K562	blood:	n/a	n/a
30	RCOR1	chr1:150980522-150981553	HepG2	liver:	n/a	n/a
31	CEBPB	chr1:150980438-150981131	A549	lung:	n/a	n/a
32	POLR2A	chr1:150980534-150981670	K562	blood:	n/a	n/a
33	ZNF143	chr1:150980516-150981127	GM12878	blood:	n/a	chr1:150980801-150980819 chr1:150980803-150980812
34	ESR1	chr1:150980442-150981036	T-47D	breast:	n/a	chr1:150980704-150980721
35	GTF2F1	chr1:150980397-150981209	Hela-S3	cervix:	n/a	n/a
36	MXI1	chr1:150980478-150981897	HepG2	liver:	n/a	n/a
37	SIN3AK20	chr1:150978184-150981996	MCF-7	breast:	n/a	n/a
38	E2F6	chr1:150980493-150981445	K562	blood:	n/a	chr1:150980880-150980889
39	FOS	chr1:150980526-150980863	MCF10A-Er-Src	breast:	n/a	chr1:150980551-150980561 chr1:150980548-150980559 chr1:150980551-150980561 chr1:150980551-150980561 chr1:150980551-150980561
40	MYBL2	chr1:150980415-150981574	HepG2	liver:	n/a	n/a
41	RFX5	chr1:150980481-150981550	Hela-S3	cervix:	n/a	chr1:150980769-150980784 chr1:150980773-150980782 chr1:150980770-150980784
42	MAZ	chr1:150980537-150981217	GM12878	blood:	n/a	chr1:150980818-150980827
43	ELF1	chr1:150980544-150981400	GM12878	blood:	n/a	chr1:150980879-150980891 chr1:150980883-150980892
44	TBL1XR1	chr1:150980526-150981097	K562	blood:	n/a	n/a
45	POLR2A	chr1:150980363-150981281	Raji	blood:	n/a	n/a
46	POLR2A	chr1:150980543-150981161	MCF10A-Er-Src	breast:	n/a	n/a
47	SIX5	chr1:150980383-150981273	A549	lung:	n/a	chr1:150980803-150980812
48	MXI1	chr1:150980226-150982457	IMR90	lung:	n/a	n/a
49	POLR2A	chr1:150980476-150981737	SK-N-MC	brain:	n/a	n/a
50	SIN3A	chr1:150980479-150981961	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150945812..150948969-chr1:150979293..150982183,4	K562	blood:
2	chr1:150974834..150982774-chr1:151014282..151023779,19	MCF-7	breast:
3	chr1:150849097..150850809-chr1:150979255..150981896,2	MCF-7	breast:
4	chr1:150550535..150554049-chr1:150976755..150981799,6	K562	blood:
5	chr1:150979021..150981360-chr1:151118629..151120745,2	K562	blood:
6	chr1:150532436..150535638-chr1:150978193..150982152,3	MCF-7	breast:
7	chr1:150980411..150982537-chr1:151106245..151107794,2	K562	blood:
8	chr1:150979291..150984938-chr1:151030285..151033653,10	K562	blood:
9	chr1:150979986..150982538-chr1:151136841..151139170,3	K562	blood:
10	chr1:150953956..150954910-chr1:150980206..150980789,4	MCF-7	breast:
11	chr1:150979099..150980863-chr1:151170963..151172486,2	MCF-7	breast:
12	chr1:150944222..150949507-chr1:150975860..150982521,8	K562	blood:
13	chr1:150977224..150980859-chr1:151016149..151020552,4	K562	blood:
14	chr1:150980465..150981394-chr1:151031769..151032709,2	K562	blood:
15	chr1:150954014..150954910-chr1:150980209..150980838,4	MCF-7	breast:
16	chr1:150334947..150337371-chr1:150979446..150982037,2	K562	blood:
17	chr1:150953914..150954774-chr1:150980327..150981076,4	MCF-7	breast:
18	chr1:150951620..150955085-chr1:150979651..150983018,4	K562	blood:
19	chr1:150979416..150982558-chr1:151006468..151010604,5	MCF-7	breast:
20	chr1:27190554..27191054-chr1:150980317..150980818,2	NB4	blood:
21	chr1:150942078..150949693-chr1:150976791..150984782,24	MCF-7	breast:
22	chr1:150952182..150958148-chr1:150976816..150982947,12	MCF-7	breast:
23	chr1:150978624..150980808-chr1:151042705..151044650,2	MCF-7	breast:
24	chr1:150978947..150982308-chr1:151041500..151045951,4	K562	blood:
25	chr1:150977392..150983338-chr1:151040807..151046211,16	MCF-7	breast:
26	chr1:150979239..150982026-chr1:151136822..151140051,3	MCF-7	breast:
27	chr1:150976723..150987587-chr1:151024685..151036322,24	MCF-7	breast:
28	chr1:150979106..150980954-chr1:151030690..151033653,4	K562	blood:
29	chr1:150939149..150940667-chr1:150979140..150981857,2	MCF-7	breast:
30	chr1:150979769..150983967-chr1:151018069..151024059,8	MCF-7	breast:
31	chr1:150979682..150982247-chr1:150996495..150999456,2	MCF-7	breast:

Variant related genes	Relation type
FAM63A	TF binding region
PRUNE	TF binding region
ENSG00000163155	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000143437	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000213190	Chromatin interaction
ENSG00000143443	Chromatin interaction
ENSG00000163141	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000143412	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000231073	Chromatin interaction
ENSG00000143434	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1545625	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1545626	0.89[ASW][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[AMR][1000 genomes]
rs2925741	0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs771197	0.89[ASW][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs771199	0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs771202	0.83[AMR][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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 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	chr1:150973600-150980800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr1:150975400-150982400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:150977400-150980600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr1:150977400-150981800	Active TSS	Esophagus	oesophagus
5	chr1:150978000-150980800	Flanking Active TSS	Dnd41	blood
6	chr1:150978000-150980800	Flanking Active TSS	K562	blood
7	chr1:150978000-150981400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr1:150978200-150980600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:150978800-150981800	Active TSS	HSMMtube	muscle
10	chr1:150979200-150980600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr1:150979200-150980800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:150979200-150981000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:150979400-150980600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:150979400-150980600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:150979400-150980600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr1:150979400-150980600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr1:150979400-150980800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:150979400-150980800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:150979400-150980800	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr1:150979400-150980800	Flanking Active TSS	Liver	Liver
21	chr1:150979400-150980800	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr1:150979400-150980800	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr1:150979400-150980800	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr1:150979400-150980800	Weak transcription	Gastric	stomach
25	chr1:150979400-150980800	Enhancers	Placenta Amnion	Placenta Amnion
26	chr1:150979400-150980800	Flanking Active TSS	Rectal Smooth Muscle	rectum
27	chr1:150979400-150980800	Flanking Active TSS	Hela-S3	cervix
28	chr1:150979400-150981000	Weak transcription	Lung	lung
29	chr1:150979400-150981000	Weak transcription	Ovary	ovary
30	chr1:150979400-150981000	Enhancers	Spleen	Spleen
31	chr1:150979600-150980600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:150979600-150980600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:150979600-150980600	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr1:150979600-150980600	Enhancers	Fetal Muscle Trunk	muscle
35	chr1:150979600-150980600	Enhancers	Fetal Thymus	thymus
36	chr1:150979600-150980800	Enhancers	Placenta	Placenta
37	chr1:150979600-150981000	Enhancers	Stomach Mucosa	stomach
38	chr1:150979800-150980600	Enhancers	Pancreas	Pancrea
39	chr1:150979800-150980600	Enhancers	Right Atrium	heart
40	chr1:150979800-150980600	Enhancers	Right Ventricle	heart
41	chr1:150979800-150980600	Enhancers	HSMM	muscle
42	chr1:150979800-150980800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:150979800-150980800	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr1:150980000-150980600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:150980000-150980600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr1:150980000-150980600	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr1:150980000-150980600	Flanking Active TSS	A549	lung
48	chr1:150980000-150980800	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr1:150980000-150980800	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr1:150980000-150980800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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