Variant report

Variant	rs72685368
Chromosome Location	chr1:78443488-78443489
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr1:78443242-78443652	GM12878	blood:	n/a	chr1:78443424-78443433 chr1:78443424-78443433
2	POLR2A	chr1:78442194-78445438	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:78443332-78446830	MCF10A-Er-Src	breast:	n/a	n/a
4	TBL1XR1	chr1:78443467-78445330	K562	blood:	n/a	n/a
5	CHD1	chr1:78443223-78445655	H1-hESC	embryonic stem cell:	n/a	chr1:78444836-78444845
6	KAP1	chr1:78443144-78445743	HEK293	kidney:	n/a	n/a
7	POLR2A	chr1:78443223-78445898	IMR90	lung:	n/a	n/a
8	POLR2A	chr1:78443129-78445525	GM12892	blood:	n/a	n/a
9	SIN3A	chr1:78443356-78445567	H1-hESC	embryonic stem cell:	n/a	n/a
10	MXI1	chr1:78443033-78446246	SK-N-SH	brain:	n/a	n/a
11	CHD1	chr1:78443338-78445594	GM12878	blood:	n/a	chr1:78444836-78444845
12	POLR2A	chr1:78442427-78445459	GM12878	blood:	n/a	n/a
13	MTA3	chr1:78443471-78445625	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:78440937-78445383	K562	blood:	n/a	n/a
15	HCFC1	chr1:78443132-78445572	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr1:78443455-78445990	SK-N-MC	brain:	n/a	n/a
17	REST	chr1:78443445-78445632	H1-neurons	neurons:	n/a	n/a
18	MXI1	chr1:78443286-78446480	IMR90	lung:	n/a	n/a
19	ATF2	chr1:78443469-78445627	GM12878	blood:	n/a	n/a
20	IRF3	chr1:78443283-78443714	HepG2	liver:	n/a	n/a
21	POLR2A	chr1:78442521-78446101	PFSK-1	brain:	n/a	n/a
22	TFAP2C	chr1:78443425-78445393	Hela-S3	cervix:	n/a	chr1:78443975-78443990 chr1:78445084-78445099
23	POLR2A	chr1:78442029-78445547	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:78443240-78446047	H1-hESC	embryonic stem cell:	n/a	n/a
25	BCLAF1	chr1:78443396-78445408	GM12878	blood:	n/a	n/a
26	IRF1	chr1:78443310-78443554	K562	blood:	n/a	n/a
27	CREB1	chr1:78443486-78445682	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:78443393-78445486	GM19099	blood:	n/a	n/a
29	POLR2A	chr1:78443452-78445474	HL-60	blood:	n/a	n/a
30	POLR2A	chr1:78443319-78445232	HepG2	liver:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:78419725..78422750-chr1:78442650..78445885,3	MCF-7	breast:
2	chr1:78411683..78415390-chr1:78442833..78445980,4	MCF-7	breast:
3	chr1:78441900..78447727-chr1:78466477..78473207,15	MCF-7	breast:
4	chr1:78165656..78168470-chr1:78443418..78445028,2	K562	blood:
5	chr1:78147609..78151437-chr1:78443386..78446443,6	K562	blood:
6	chr1:78223072..78225558-chr1:78443212..78444913,3	K562	blood:
7	chr1:78441362..78443969-chr1:78545013..78547502,2	K562	blood:
8	chr1:78442485..78444153-chr8:102209563..102211525,2	MCF-7	breast:
9	chr1:78442786..78443510-chr1:78579652..78580579,4	MCF-7	breast:
10	chr1:78441980..78446801-chr1:78467462..78471771,12	MCF-7	breast:

No data

Variant related genes	Relation type
GIPC2	TF binding region
DNAJB4	TF binding region
ENSG00000162616	Chromatin interaction
ENSG00000077254	Chromatin interaction
ENSG00000162613	Chromatin interaction
ENSG00000273338	Chromatin interaction
ENSG00000036549	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1039863	0.92[ASN][1000 genomes]
rs10873961	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10873962	0.83[ASN][1000 genomes]
rs10873963	0.83[ASN][1000 genomes]
rs11162401	0.98[ASN][1000 genomes]
rs1166696	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1166699	0.91[ASN][1000 genomes]
rs1166700	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11805942	0.98[ASN][1000 genomes]
rs11806130	0.96[ASN][1000 genomes]
rs11811805	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1510244	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17101101	0.98[ASN][1000 genomes]
rs1749911	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1749913	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1780044	0.91[ASN][1000 genomes]
rs1780045	0.91[ASN][1000 genomes]
rs1780047	0.91[ASN][1000 genomes]
rs1780048	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1780052	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2296452	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296454	0.98[ASN][1000 genomes]
rs3736909	0.98[ASN][1000 genomes]
rs3767024	0.98[ASN][1000 genomes]
rs3767025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4083559	0.90[ASN][1000 genomes]
rs4107671	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4483454	0.91[ASN][1000 genomes]
rs4543852	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6424648	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6424653	0.92[ASN][1000 genomes]
rs6680447	0.88[ASN][1000 genomes]
rs6699513	0.83[ASN][1000 genomes]
rs6702465	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72685363	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72685364	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7520255	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7523874	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7524504	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9661687	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9662129	0.91[ASN][1000 genomes]
rs9729146	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv518855	chr1:78416669-78456355	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 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	chr1:78433800-78443600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:78440200-78443600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
3	chr1:78440200-78444000	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr1:78440200-78444400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
5	chr1:78440200-78445200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:78440800-78444400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
7	chr1:78441200-78443600	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr1:78441200-78443800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr1:78441200-78444600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:78441200-78446200	Active TSS	Aorta	Aorta
11	chr1:78441400-78443600	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:78441400-78444000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
13	chr1:78441400-78444000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:78441400-78446800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:78441600-78446000	Active TSS	Colonic Mucosa	Colon
16	chr1:78441800-78445600	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr1:78441800-78446200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:78442000-78446200	Active TSS	Brain Angular Gyrus	brain
19	chr1:78442000-78446800	Active TSS	GM12878-XiMat	blood
20	chr1:78442000-78447200	Active TSS	A549	lung
21	chr1:78442200-78443600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:78442200-78443800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:78442200-78443800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
24	chr1:78442200-78445800	Active TSS	Duodenum Mucosa	Duodenum
25	chr1:78442200-78446600	Active TSS	H9 Cell Line	embryonic stem cell
26	chr1:78442400-78443800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr1:78442400-78443800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
28	chr1:78442400-78443800	Flanking Active TSS	Liver	Liver
29	chr1:78442400-78446000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:78442400-78446200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:78442600-78443600	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
32	chr1:78442600-78443800	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr1:78442600-78443800	Weak transcription	Spleen	Spleen
34	chr1:78442600-78445600	Active TSS	Stomach Smooth Muscle	stomach
35	chr1:78442600-78446000	Active TSS	Esophagus	oesophagus
36	chr1:78442600-78446000	Active TSS	Gastric	stomach
37	chr1:78442600-78446000	Active TSS	Ovary	ovary
38	chr1:78442600-78446200	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr1:78442600-78446200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:78442600-78446200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:78442600-78446200	Active TSS	Psoas Muscle	Psoas
42	chr1:78442600-78446400	Active TSS	H1 Cell Line	embryonic stem cell
43	chr1:78442600-78446600	Active TSS	Right Atrium	heart
44	chr1:78442600-78447000	Active TSS	Right Ventricle	heart
45	chr1:78442800-78443800	Active TSS	HepG2	liver
46	chr1:78442800-78444000	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr1:78442800-78444000	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr1:78442800-78445800	Active TSS	Brain Cingulate Gyrus	brain
49	chr1:78442800-78445800	Active TSS	Fetal Heart	heart
50	chr1:78442800-78446000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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