Variant report

Variant	rs72804674
Chromosome Location	chr2:54682941-54682942
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	TAF1	chr2:54682875-54683351	H1-hESC	embryonic stem cell:	n/a	n/a
2	MYBL2	chr2:54681501-54683343	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:54682918-54684551	A549	lung:	n/a	n/a
4	TAF1	chr2:54682934-54683755	A549	lung:	n/a	n/a
5	ZBTB7A	chr2:54682908-54684675	ECC-1	luminal epithelium:	n/a	chr2:54683663-54683671 chr2:54684493-54684507 chr2:54684498-54684507
6	MAX	chr2:54682882-54683689	A549	lung:	n/a	chr2:54682934-54682942
7	POLR2A	chr2:54682588-54683692	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr2:54682189-54685375	H1-neurons	neurons:	n/a	n/a
9	FOSL2	chr2:54682753-54683271	A549	lung:	n/a	chr2:54682849-54682858
10	POLR2A	chr2:54682763-54683744	U87	brain:	n/a	n/a
11	MYBL2	chr2:54681631-54683715	HepG2	liver:	n/a	n/a
12	MXI1	chr2:54682730-54686241	IMR90	lung:	n/a	n/a
13	HEY1	chr2:54681566-54683738	HepG2	liver:	n/a	chr2:54683583-54683598 chr2:54683492-54683507
14	EP300	chr2:54682900-54683593	HepG2	liver:	n/a	chr2:54683504-54683520
15	EP300	chr2:54682806-54683685	SK-N-SH_RA	brain:	n/a	chr2:54683630-54683639 chr2:54683504-54683520
16	RCOR1	chr2:54682837-54683787	HepG2	liver:	n/a	n/a
17	POLR2A	chr2:54682165-54683785	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr2:54682900-54683050	SK-N-SH_RA	brain:	n/a	n/a
19	HA-E2F1	chr2:54682786-54683304	MCF-7	breast:	n/a	n/a
20	ARID3A	chr2:54682853-54683244	HepG2	liver:	n/a	n/a
21	POLR2A	chr2:54682919-54683353	HepG2	liver:	n/a	n/a
22	SP1	chr2:54682897-54683565	A549	lung:	n/a	chr2:54683072-54683081 chr2:54683543-54683557 chr2:54683072-54683082 chr2:54683073-54683082 chr2:54683071-54683083 chr2:54683071-54683083 chr2:54683072-54683081
23	YY1	chr2:54682886-54684411	HepG2	liver:	n/a	chr2:54684224-54684238 chr2:54683188-54683199 chr2:54684135-54684144 chr2:54684136-54684147 chr2:54683992-54684006 chr2:54683718-54683727 chr2:54684122-54684133
24	TCF12	chr2:54682609-54683757	A549	lung:	n/a	n/a
25	POLR2A	chr2:54682862-54683729	PANC-1	pancreas:	n/a	n/a
26	CTCF	chr2:54682940-54683090	HBMEC	blood vessel:	n/a	n/a
27	POLR2A	chr2:54681650-54683349	HepG2	liver:	n/a	n/a
28	RAD21	chr2:54682823-54683310	SK-N-SH_RA	brain:	n/a	n/a
29	ZNF263	chr2:54682800-54685302	HEK293-T-REx	kidney:	n/a	chr2:54683982-54683991 chr2:54683734-54683743 chr2:54683611-54683620
30	RFX5	chr2:54682895-54683642	HepG2	liver:	n/a	chr2:54683433-54683448
31	CTCF	chr2:54682820-54682970	A549	lung:	n/a	n/a
32	POLR2A	chr2:54682763-54683750	U87	brain:	n/a	n/a
33	CTBP2	chr2:54682379-54685140	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr2:54682873-54684758	Gliobla	brain:	n/a	n/a
35	MBD4	chr2:54682085-54683332	HepG2	liver:	n/a	n/a
36	SP1	chr2:54682882-54683686	A549	lung:	n/a	chr2:54683072-54683081 chr2:54683543-54683557 chr2:54683072-54683082 chr2:54683073-54683082 chr2:54683071-54683083 chr2:54683071-54683083 chr2:54683072-54683081
37	SIN3AK20	chr2:54682810-54683313	PANC-1	pancreas:	n/a	n/a
38	CTCF	chr2:54682920-54683070	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr2:54682743-54683355	SK-N-SH	brain:	n/a	n/a
40	FOXA1	chr2:54682896-54683482	HepG2	liver:	n/a	n/a
41	REST	chr2:54682752-54683356	HepG2	liver:	n/a	n/a
42	TAF1	chr2:54682700-54683643	H1-neurons	neurons:	n/a	n/a
43	CTCF	chr2:54682900-54683050	HPAF	blood vessel:	n/a	n/a
44	CTCF	chr2:54682900-54683050	BJ	skin:	n/a	n/a
45	POLR2A	chr2:54682691-54683866	HUVEC	blood vessel:	n/a	n/a
46	MXI1	chr2:54682590-54684279	HepG2	liver:	n/a	n/a
47	POLR2A	chr2:54682923-54683741	PANC-1	pancreas:	n/a	n/a
48	REST	chr2:54682890-54683744	H1-neurons	neurons:	n/a	n/a
49	POLR2A	chr2:54682683-54683354	HepG2	liver:	n/a	n/a
50	MAX	chr2:54682863-54683805	HepG2	liver:	n/a	chr2:54682934-54682942

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54341520..54343821-chr2:54682367..54684141,3	MCF-7	breast:
2	chr2:54663282..54665058-chr2:54681463..54683178,2	MCF-7	breast:

Variant related genes	Relation type
SPTBN1	TF binding region
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10181826	0.85[EUR][1000 genomes]
rs10496030	0.87[EUR][1000 genomes]
rs11125539	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11694121	0.90[EUR][1000 genomes]
rs12470235	0.87[EUR][1000 genomes]
rs13393949	0.85[EUR][1000 genomes]
rs35636918	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4505569	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56257354	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72804673	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7419821	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7574630	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv3403234	chr2:54681448-54686246	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3407657	chr2:54682273-54685021	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv3392501	chr2:54682473-54685646	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54681800-54683200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:54682000-54683000	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr2:54682000-54685000	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr2:54682000-54685400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr2:54682000-54685400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr2:54682000-54685600	Active TSS	Brain Substantia Nigra	brain
7	chr2:54682000-54686200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr2:54682200-54683000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr2:54682200-54683000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
10	chr2:54682200-54683000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:54682200-54683000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:54682200-54683000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
13	chr2:54682200-54683000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr2:54682200-54683000	Flanking Active TSS	Fetal Muscle Trunk	muscle
15	chr2:54682200-54683000	Flanking Active TSS	Fetal Muscle Leg	muscle
16	chr2:54682200-54683000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
17	chr2:54682200-54683000	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr2:54682200-54683000	Flanking Active TSS	A549	lung
19	chr2:54682200-54683000	Flanking Active TSS	HUVEC	blood vessel
20	chr2:54682200-54683000	Flanking Active TSS	Osteobl	bone
21	chr2:54682200-54683200	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr2:54682200-54683200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr2:54682200-54683200	Flanking Active TSS	Liver	Liver
24	chr2:54682200-54683200	Bivalent/Poised TSS	HepG2	liver
25	chr2:54682200-54685000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:54682200-54685200	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr2:54682200-54685400	Active TSS	H9 Cell Line	embryonic stem cell
28	chr2:54682200-54685400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:54682200-54685600	Active TSS	Fetal Kidney	kidney
30	chr2:54682200-54685800	Active TSS	Brain Germinal Matrix	brain
31	chr2:54682200-54686000	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr2:54682200-54686200	Active TSS	Left Ventricle	heart
33	chr2:54682200-54686200	Active TSS	NHDF-Ad	bronchial
34	chr2:54682200-54686400	Active TSS	Aorta	Aorta
35	chr2:54682200-54687000	Active TSS	Ovary	ovary
36	chr2:54682200-54687000	Active TSS	Psoas Muscle	Psoas
37	chr2:54682200-54687600	Active TSS	Right Atrium	heart
38	chr2:54682400-54683000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:54682400-54683000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:54682400-54683000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:54682400-54683000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
42	chr2:54682400-54683000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:54682400-54683000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
44	chr2:54682400-54683000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:54682400-54683000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:54682400-54683000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr2:54682400-54683000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr2:54682400-54683000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:54682400-54683000	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:54682400-54683000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum

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