Variant report

Variant	rs72746037
Chromosome Location	chr1:221509335-221509336
allele	A/C
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	GTF2F1	chr1:221508338-221509564	Hela-S3	cervix:	n/a	n/a
2	SMC3	chr1:221508329-221509658	Hela-S3	cervix:	n/a	n/a
3	KAP1	chr1:221508480-221509430	U2OS	brain:	n/a	n/a
4	MAZ	chr1:221508656-221509639	Hela-S3	cervix:	n/a	n/a
5	TCF7L2	chr1:221508415-221509642	HEK293	kidney:	n/a	chr1:221508628-221508637 chr1:221508939-221508953 chr1:221508780-221508787
6	STAT3	chr1:221508422-221509665	Hela-S3	cervix:	n/a	chr1:221508628-221508637 chr1:221509036-221509048 chr1:221508728-221508736
7	TCF7L2	chr1:221508375-221509675	Hela-S3	cervix:	n/a	chr1:221508628-221508637 chr1:221508939-221508953 chr1:221508780-221508787
8	BRCA1	chr1:221508514-221509639	Hela-S3	cervix:	n/a	n/a
9	PBX3	chr1:221508390-221509386	SK-N-SH	brain:	n/a	chr1:221508764-221508775 chr1:221508988-221508997
10	TFAP2C	chr1:221508619-221510021	Hela-S3	cervix:	n/a	n/a
11	TCF12	chr1:221508300-221510023	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr1:221509051-221509372	Hela-S3	cervix:	n/a	n/a
13	NFIC	chr1:221508408-221509998	SK-N-SH	brain:	n/a	n/a
14	CEBPB	chr1:221508246-221509821	Hela-S3	cervix:	n/a	chr1:221508741-221508752 chr1:221508743-221508754
15	TCF12	chr1:221508347-221510013	SK-N-SH	brain:	n/a	n/a
16	USF2	chr1:221508824-221509608	Hela-S3	cervix:	n/a	n/a
17	MAX	chr1:221508559-221509683	Hela-S3	cervix:	n/a	chr1:221508627-221508636
18	JUND	chr1:221508307-221509954	SK-N-SH	brain:	n/a	chr1:221508624-221508635 chr1:221509644-221509652 chr1:221508627-221508637 chr1:221508627-221508637 chr1:221508628-221508637 chr1:221508626-221508637 chr1:221508627-221508637 chr1:221508627-221508637
19	RAD21	chr1:221508454-221509845	Hela-S3	cervix:	n/a	n/a
20	YY1	chr1:221508692-221509402	SK-N-SH	brain:	n/a	n/a
21	EP300	chr1:221508288-221509980	SK-N-SH	brain:	n/a	chr1:221508984-221508997 chr1:221509733-221509747 chr1:221508627-221508636
22	POLR2A	chr1:221508462-221509489	U87	brain:	n/a	n/a
23	POLR2A	chr1:221508577-221509868	Hela-S3	cervix:	n/a	n/a
24	JUN	chr1:221508414-221509838	Hela-S3	cervix:	n/a	chr1:221508624-221508635 chr1:221509644-221509652 chr1:221508627-221508637 chr1:221508627-221508637 chr1:221508628-221508637 chr1:221508627-221508637 chr1:221508627-221508637
25	RFX5	chr1:221508457-221509904	Hela-S3	cervix:	n/a	n/a
26	SMARCC1	chr1:221508335-221509924	Hela-S3	cervix:	n/a	n/a
27	CHD2	chr1:221508550-221509683	Hela-S3	cervix:	n/a	n/a
28	TAF1	chr1:221509175-221509345	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr1:221508426-221509757	MCF10A-Er-Src	breast:	n/a	n/a
30	RCOR1	chr1:221508238-221509539	Hela-S3	cervix:	n/a	n/a
31	KAP1	chr1:221507915-221509476	HEK293	kidney:	n/a	n/a
32	TEAD4	chr1:221508492-221509490	SK-N-SH	brain:	n/a	n/a
33	MYC	chr1:221508434-221509650	Hela-S3	cervix:	n/a	chr1:221508627-221508636
34	PBX3	chr1:221508386-221509365	SK-N-SH	brain:	n/a	chr1:221508764-221508775 chr1:221508988-221508997
35	TEAD4	chr1:221508397-221509435	SK-N-SH	brain:	n/a	n/a
36	PRDM1	chr1:221508587-221509928	Hela-S3	cervix:	n/a	chr1:221509735-221509744 chr1:221508628-221508637 chr1:221509730-221509745 chr1:221508627-221508636
37	GATA3	chr1:221508240-221510017	SK-N-SH	brain:	n/a	chr1:221508972-221508985 chr1:221509083-221509100
38	TFAP2A	chr1:221508604-221509903	Hela-S3	cervix:	n/a	chr1:221509834-221509846
39	POLR2A	chr1:221508503-221509961	U87	brain:	n/a	n/a
40	MAFK	chr1:221508545-221509849	Hela-S3	cervix:	n/a	n/a
41	JUND	chr1:221508417-221509826	Hela-S3	cervix:	n/a	chr1:221508624-221508635 chr1:221509644-221509652 chr1:221508627-221508637 chr1:221508627-221508637 chr1:221508628-221508637 chr1:221508626-221508637 chr1:221508627-221508637 chr1:221508627-221508637
42	POLR2A	chr1:221508973-221509413	Hela-S3	cervix:	n/a	n/a
43	EP300	chr1:221508485-221509437	SK-N-SH	brain:	n/a	chr1:221508984-221508997 chr1:221508627-221508636
44	JUND	chr1:221508297-221509461	SK-N-SH	brain:	n/a	chr1:221508624-221508635 chr1:221508627-221508637 chr1:221508627-221508637 chr1:221508628-221508637 chr1:221508626-221508637 chr1:221508627-221508637 chr1:221508627-221508637
45	POLR2A	chr1:221508497-221509967	U87	brain:	n/a	n/a
46	ZKSCAN1	chr1:221508486-221509817	Hela-S3	cervix:	n/a	n/a
47	EP300	chr1:221508377-221509808	Hela-S3	cervix:	n/a	chr1:221508984-221508997 chr1:221509733-221509747 chr1:221508627-221508636
48	MAX	chr1:221508322-221509816	Hela-S3	cervix:	n/a	chr1:221508627-221508636
49	GATA2	chr1:221508744-221509402	SH-SY5Y	brain:	n/a	chr1:221508972-221508985 chr1:221509083-221509100
50	FOS	chr1:221508459-221509355	Hela-S3	cervix:	n/a	chr1:221508624-221508635 chr1:221508627-221508637 chr1:221508627-221508637 chr1:221508628-221508637 chr1:221508627-221508637 chr1:221508627-221508637

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:221508805..221509424-chr9:133319842..133320722,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DUSP10-5	chr1:221509205-221509638	NR_024236
2	lnc-DUSP10-5	chr1:221509205-221509638	ENSG00000234754

Variant related genes	Relation type
ENSG00000234754	TF binding region
ENSG00000130707	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10489951	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10735499	0.87[ASN][1000 genomes]
rs11118705	0.96[ASN][1000 genomes]
rs11118706	0.96[ASN][1000 genomes]
rs12084980	0.96[ASN][1000 genomes]
rs3123736	0.96[ASN][1000 genomes]
rs3131543	0.96[ASN][1000 genomes]
rs41349545	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4517352	0.96[ASN][1000 genomes]
rs4609434	0.96[ASN][1000 genomes]
rs4846344	0.81[ASN][1000 genomes]
rs6679291	0.89[ASN][1000 genomes]
rs6697087	0.82[ASN][1000 genomes]
rs72744240	0.82[ASN][1000 genomes]
rs72744253	0.82[ASN][1000 genomes]
rs72744259	0.86[ASN][1000 genomes]
rs72744270	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72746040	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72746060	0.93[ASN][1000 genomes]
rs72746061	0.93[ASN][1000 genomes]
rs72746075	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs731372	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548451	0.81[ASN][1000 genomes]
rs7552266	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221506400-221509800	Enhancers	Fetal Stomach	stomach
2	chr1:221506600-221509600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:221507000-221510000	Enhancers	Ovary	ovary
4	chr1:221507200-221509600	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr1:221507200-221509600	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr1:221507200-221509800	Enhancers	Brain Cingulate Gyrus	brain
7	chr1:221507200-221510000	Enhancers	Placenta	Placenta
8	chr1:221507200-221511000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:221507400-221510600	Enhancers	Colon Smooth Muscle	Colon
10	chr1:221507800-221509400	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr1:221507800-221509600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:221507800-221509600	Enhancers	Right Atrium	heart
13	chr1:221507800-221509800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:221507800-221511200	Enhancers	Fetal Lung	lung
15	chr1:221508000-221509400	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr1:221508000-221509800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:221508000-221510000	Flanking Active TSS	Hela-S3	cervix
18	chr1:221508200-221509400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:221508200-221509400	Weak transcription	Psoas Muscle	Psoas
20	chr1:221508200-221509800	Enhancers	NH-A	brain
21	chr1:221508400-221509400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:221508400-221509400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:221508400-221509400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr1:221508400-221509400	Enhancers	HMEC	breast
25	chr1:221508400-221509600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:221508400-221509600	Enhancers	Fetal Kidney	kidney
27	chr1:221508400-221509800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:221508400-221509800	Flanking Active TSS	NHDF-Ad	bronchial
29	chr1:221508400-221509800	Flanking Active TSS	Osteobl	bone
30	chr1:221508600-221509600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:221508600-221510200	Enhancers	Fetal Muscle Leg	muscle
32	chr1:221508800-221509400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:221508800-221509400	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr1:221508800-221509400	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr1:221508800-221509400	Enhancers	Liver	Liver
36	chr1:221508800-221509600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:221508800-221509600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr1:221508800-221509600	Flanking Active TSS	Brain Anterior Caudate	brain
39	chr1:221508800-221509600	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr1:221508800-221509600	Flanking Active TSS	HSMMtube	muscle
41	chr1:221508800-221509600	Flanking Active TSS	NHLF	lung
42	chr1:221508800-221509800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:221509000-221509400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:221509000-221509600	Enhancers	Aorta	Aorta
45	chr1:221509000-221509800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:221509000-221510000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:221509000-221510400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:221509000-221510400	Enhancers	Rectal Smooth Muscle	rectum
49	chr1:221509200-221509400	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr1:221509200-221509400	Flanking Active TSS	Brain Substantia Nigra	brain

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