Variant report

Variant	rs10888978
Chromosome Location	chr1:57001009-57001010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr1:57000570-57001415	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP1	chr1:57000898-57001382	H1-hESC	embryonic stem cell:	n/a	chr1:57001245-57001252
3	CHD1	chr1:57000866-57001224	H1-hESC	embryonic stem cell:	n/a	n/a
4	MYC	chr1:57000742-57001595	H1-hESC	embryonic stem cell:	n/a	n/a
5	SP1	chr1:57000909-57001537	H1-hESC	embryonic stem cell:	n/a	chr1:57001245-57001252
6	MAX	chr1:57000684-57001530	H1-hESC	embryonic stem cell:	n/a	n/a
7	TBP	chr1:57000989-57001521	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:56999856-57001768	PFSK-1	brain:	n/a	n/a
9	TEAD4	chr1:57000997-57001642	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:56999993-57001990	H1-hESC	embryonic stem cell:	n/a	n/a
11	GTF2F1	chr1:57000967-57001430	H1-hESC	embryonic stem cell:	n/a	n/a
12	CEBPB	chr1:57001009-57001454	H1-hESC	embryonic stem cell:	n/a	n/a
13	USF1	chr1:57000914-57001415	H1-hESC	embryonic stem cell:	n/a	n/a
14	USF1	chr1:57000960-57001386	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr1:57000729-57001894	H1-hESC	embryonic stem cell:	n/a	n/a
16	ATF2	chr1:57000839-57001494	H1-hESC	embryonic stem cell:	n/a	n/a
17	YY1	chr1:57000941-57001313	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr1:57000631-57001512	H1-hESC	embryonic stem cell:	n/a	n/a
19	ATF2	chr1:57000803-57001526	H1-hESC	embryonic stem cell:	n/a	n/a
20	MXI1	chr1:57000822-57001442	H1-hESC	embryonic stem cell:	n/a	n/a
21	YY1	chr1:57000892-57001444	H1-hESC	embryonic stem cell:	n/a	n/a
22	ZNF143	chr1:57000982-57001613	H1-hESC	embryonic stem cell:	n/a	chr1:57001375-57001394
23	EP300	chr1:57000956-57001430	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr1:56998973-57004163	HepG2	liver:	n/a	n/a
25	SIN3A	chr1:57000889-57001468	H1-hESC	embryonic stem cell:	n/a	n/a
26	USF2	chr1:57000974-57001703	H1-hESC	embryonic stem cell:	n/a	n/a

No data

Variant related genes	Relation type
RPL21P23	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10443239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10493211	1.00[JPT][hapmap]
rs10789026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11206831	1.00[JPT][hapmap]
rs11206832	1.00[JPT][hapmap]
rs11206834	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11206835	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11206838	1.00[JPT][hapmap]
rs11576602	1.00[JPT][hapmap]
rs11582172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134109	1.00[JPT][hapmap]
rs12137700	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12402226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12406517	1.00[JPT][hapmap]
rs1572057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2404717	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3738570	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3927762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528118	1.00[JPT][hapmap]
rs7551402	1.00[JPT][hapmap]
rs8016	1.00[JPT][hapmap]
rs869934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56967000-57002000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:56987000-57015000	Genic enhancers	NHDF-Ad	bronchial
3	chr1:56990000-57004000	Genic enhancers	Liver	Liver
4	chr1:56992000-57001200	Weak transcription	Spleen	Spleen
5	chr1:56992800-57011200	Weak transcription	Stomach Mucosa	stomach
6	chr1:56993000-57004600	Weak transcription	Hela-S3	cervix
7	chr1:56993200-57001400	Enhancers	Right Atrium	heart
8	chr1:56993600-57007800	Weak transcription	Primary B cells from cord blood	blood
9	chr1:56993800-57004200	Weak transcription	NH-A	brain
10	chr1:56994000-57001200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:56994000-57004000	Weak transcription	HUVEC	blood vessel
12	chr1:56994000-57012400	Weak transcription	Fetal Brain Male	brain
13	chr1:56994000-57012800	Weak transcription	Fetal Brain Female	brain
14	chr1:56994200-57001200	Weak transcription	Dnd41	blood
15	chr1:56994200-57004400	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr1:56994400-57002600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:56995000-57003400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr1:56995000-57003600	Strong transcription	Osteobl	bone
19	chr1:56995200-57003800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:56995600-57004600	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:56995800-57004000	Genic enhancers	HepG2	liver
22	chr1:56996000-57001200	Enhancers	Right Ventricle	heart
23	chr1:56996000-57002800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
24	chr1:56996200-57003000	Genic enhancers	H1 Cell Line	embryonic stem cell
25	chr1:56996200-57003000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
26	chr1:56996200-57003000	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr1:56996600-57004000	Strong transcription	HSMM	muscle
28	chr1:56996600-57005200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:56996800-57003000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:56997000-57001800	Genic enhancers	Adipose Nuclei	Adipose
31	chr1:56997000-57003400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:56997200-57002600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:56997200-57004600	Genic enhancers	Placenta	Placenta
34	chr1:56997400-57002600	Strong transcription	Lung	lung
35	chr1:56997400-57002800	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr1:56997600-57002000	Genic enhancers	Fetal Thymus	thymus
37	chr1:56997600-57004400	Genic enhancers	Fetal Muscle Leg	muscle
38	chr1:56997800-57002600	Genic enhancers	Brain Anterior Caudate	brain
39	chr1:56997800-57003600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
40	chr1:56998000-57002800	Genic enhancers	Left Ventricle	heart
41	chr1:56998600-57002200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr1:56998600-57003800	Strong transcription	Fetal Stomach	stomach
43	chr1:56998800-57001400	Weak transcription	Small Intestine	intestine
44	chr1:56998800-57002000	Genic enhancers	Thymus	Thymus
45	chr1:56998800-57002600	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr1:56999000-57001600	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:56999000-57002400	Strong transcription	Aorta	Aorta
48	chr1:56999200-57001200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:56999200-57001200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr1:56999200-57001200	Strong transcription	A549	lung

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