Variant report

Variant	rs72795440
Chromosome Location	chr2:55242456-55242457
allele	C/T
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	chr2:55242182-55242457	T-47D	breast:	n/a	n/a
2	SMC3	chr2:55242161-55242472	K562	blood:	n/a	chr2:55242273-55242287
3	CTCF	chr2:55242076-55242493	A549	lung:	n/a	chr2:55242272-55242288 chr2:55242273-55242294 chr2:55242276-55242284 chr2:55242271-55242289
4	POLR2A	chr2:55242126-55242472	A549	lung:	n/a	n/a
5	RAD21	chr2:55242104-55242503	GM12878	blood:	n/a	chr2:55242272-55242291
6	RAD21	chr2:55242110-55242484	A549	lung:	n/a	chr2:55242272-55242291
7	RAD21	chr2:55242158-55242481	ECC-1	luminal epithelium:	n/a	chr2:55242272-55242291
8	CTCF	chr2:55242099-55242466	A549	lung:	n/a	chr2:55242272-55242288 chr2:55242273-55242294 chr2:55242276-55242284 chr2:55242271-55242289
9	POLR2A	chr2:55242232-55242457	K562	blood:	n/a	n/a
10	POLR2A	chr2:55242195-55242480	HUVEC	blood vessel:	n/a	n/a
11	RAD21	chr2:55242072-55242508	HepG2	liver:	n/a	chr2:55242272-55242291
12	RAD21	chr2:55241982-55242534	HepG2	liver:	n/a	chr2:55242272-55242291
13	USF2	chr2:55242190-55242458	Hela-S3	cervix:	n/a	n/a
14	RAD21	chr2:55242037-55242463	SK-N-SH_RA	brain:	n/a	chr2:55242272-55242291
15	RAD21	chr2:55241926-55242652	MCF-7	breast:	n/a	chr2:55242272-55242291
16	CTCF	chr2:55242092-55242480	IMR90	lung:	n/a	chr2:55242272-55242288 chr2:55242273-55242294 chr2:55242276-55242284 chr2:55242271-55242289
17	RAD21	chr2:55242079-55242522	ECC-1	luminal epithelium:	n/a	chr2:55242272-55242291
18	SMC3	chr2:55242106-55242486	Hela-S3	cervix:	n/a	chr2:55242273-55242287
19	USF1	chr2:55242060-55242479	A549	lung:	n/a	n/a
20	SETDB1	chr2:55242282-55242874	U2OS	brain:	n/a	n/a
21	CTCF	chr2:55241957-55242583	HCT-116	colon:	n/a	chr2:55242272-55242288 chr2:55242273-55242294 chr2:55242276-55242284 chr2:55242271-55242289
22	RAD21	chr2:55241935-55242581	HCT-116	colon:	n/a	chr2:55242272-55242291
23	POLR2A	chr2:55242102-55242461	PANC-1	pancreas:	n/a	n/a
24	RAD21	chr2:55241991-55242535	MCF-7	breast:	n/a	chr2:55242272-55242291
25	TCF12	chr2:55242035-55242552	SK-N-SH	brain:	n/a	n/a
26	RAD21	chr2:55242007-55242604	HCT-116	colon:	n/a	chr2:55242272-55242291
27	CTCF	chr2:55241871-55242943	A549	lung:	n/a	chr2:55242272-55242288 chr2:55242273-55242294 chr2:55242276-55242284 chr2:55242271-55242289
28	CTCF	chr2:55241910-55243022	SK-N-SH	brain:	n/a	chr2:55242272-55242288 chr2:55242273-55242294 chr2:55242276-55242284 chr2:55242271-55242289
29	SMC3	chr2:55242059-55242490	HepG2	liver:	n/a	chr2:55242273-55242287
30	RAD21	chr2:55242140-55242470	GM12878	blood:	n/a	chr2:55242272-55242291
31	SMC3	chr2:55242070-55242659	SK-N-SH	brain:	n/a	chr2:55242273-55242287
32	RAD21	chr2:55242099-55242484	H1-hESC	embryonic stem cell:	n/a	chr2:55242272-55242291
33	RAD21	chr2:55241942-55242544	A549	lung:	n/a	chr2:55242272-55242291
34	RAD21	chr2:55242068-55242504	Hela-S3	cervix:	n/a	chr2:55242272-55242291
35	CTCF	chr2:55242084-55242487	GM12878	blood:	n/a	chr2:55242272-55242288 chr2:55242273-55242294 chr2:55242276-55242284 chr2:55242271-55242289
36	RAD21	chr2:55242142-55242458	K562	blood:	n/a	chr2:55242272-55242291
37	CTCF	chr2:55242001-55242599	HCT-116	colon:	n/a	chr2:55242272-55242288 chr2:55242273-55242294 chr2:55242276-55242284 chr2:55242271-55242289
38	RAD21	chr2:55242027-55242610	A549	lung:	n/a	chr2:55242272-55242291
39	CTCF	chr2:55242107-55242473	K562	blood:	n/a	chr2:55242272-55242288 chr2:55242273-55242294 chr2:55242276-55242284 chr2:55242271-55242289
40	RAD21	chr2:55242100-55242470	IMR90	lung:	n/a	chr2:55242272-55242291
41	RAD21	chr2:55241961-55243096	SK-N-SH	brain:	n/a	chr2:55242272-55242291
42	POLR2A	chr2:55242159-55242461	HCT-116	colon:	n/a	n/a
43	GATA2	chr2:55242198-55242460	SH-SY5Y	brain:	n/a	n/a
44	RAD21	chr2:55242053-55242489	H1-hESC	embryonic stem cell:	n/a	chr2:55242272-55242291
45	MXI1	chr2:55242133-55242459	HepG2	liver:	n/a	n/a
46	CTCF	chr2:55241983-55242561	MCF-7	breast:	n/a	chr2:55242272-55242288 chr2:55242273-55242294 chr2:55242276-55242284 chr2:55242271-55242289
47	POLR2A	chr2:55242036-55242531	SK-N-SH	brain:	n/a	n/a
48	GATA3	chr2:55242146-55242478	T-47D	breast:	n/a	n/a
49	ARID3A	chr2:55242061-55242915	HepG2	liver:	n/a	n/a
50	CTCF	chr2:55242017-55242466	HepG2	liver:	n/a	chr2:55242272-55242288 chr2:55242273-55242294 chr2:55242276-55242284 chr2:55242271-55242289

No.	Distal block	Cell Line	Cell type
1	chr2:55240957..55243233-chr2:55273939..55276356,2	K562	blood:
2	chr2:55241892..55242863-chr2:55275366..55276289,2	MCF-7	breast:
3	chr10:52043739..52044593-chr2:55242128..55242713,2	K562	blood:
4	chr2:55241176..55242945-chr2:55276344..55278140,2	MCF-7	breast:
5	chr2:55241899..55242723-chr2:55402448..55403306,4	MCF-7	breast:
6	chr2:55241818..55242793-chr2:55395477..55396356,4	MCF-7	breast:
7	chr2:55242047..55242761-chr2:55395804..55396365,2	K562	blood:
8	chr2:55242189..55242730-chr2:55402423..55403350,2	K562	blood:
9	chr2:55236989..55239116-chr2:55240470..55242602,2	K562	blood:
10	chr2:55241817..55242787-chr2:55276175..55276850,2	MCF-7	breast:
11	chr2:55241702..55243264-chr2:55276241..55278692,2	MCF-7	breast:

Variant related genes	Relation type
RTN4	TF binding region
RNU6-433P	TF binding region
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10170340	0.88[ASN][1000 genomes]
rs10189379	0.93[ASN][1000 genomes]
rs12464070	0.87[AFR][1000 genomes]
rs12464447	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12464595	0.92[ASN][1000 genomes]
rs12475787	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12475904	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12477711	0.84[AFR][1000 genomes]
rs12479297	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17046570	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17046594	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17347089	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17418675	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2241959	0.83[EUR][1000 genomes]
rs2864049	0.83[ASN][1000 genomes]
rs35826668	0.83[AFR][1000 genomes]
rs55659423	0.83[EUR][1000 genomes]
rs55698303	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55993793	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56013263	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545467	0.87[ASN][1000 genomes]
rs6713935	0.88[AFR][1000 genomes]
rs67156582	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6730728	0.87[ASN][1000 genomes]
rs72795431	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7584354	0.87[ASN][1000 genomes]
rs7584386	0.87[ASN][1000 genomes]
rs7601625	0.97[ASN][1000 genomes]
rs887	0.82[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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
2	chr2:55232200-55244800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:55234800-55244800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:55234800-55246000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:55236800-55243400	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr2:55237000-55243600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr2:55237400-55242800	Enhancers	HSMMtube	muscle
8	chr2:55237600-55243600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:55237600-55246000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:55237600-55247800	Weak transcription	Left Ventricle	heart
11	chr2:55237600-55249600	Weak transcription	Gastric	stomach
12	chr2:55237600-55250200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:55237600-55258600	Weak transcription	Ovary	ovary
14	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
15	chr2:55237800-55242800	Enhancers	Brain Substantia Nigra	brain
16	chr2:55237800-55242800	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr2:55237800-55242800	Enhancers	Rectal Smooth Muscle	rectum
18	chr2:55237800-55243000	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr2:55237800-55243400	Enhancers	Osteobl	bone
20	chr2:55237800-55243600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:55237800-55243600	Enhancers	Brain Hippocampus Middle	brain
22	chr2:55238000-55243000	Enhancers	Adipose Nuclei	Adipose
23	chr2:55238200-55245800	Weak transcription	Brain Germinal Matrix	brain
24	chr2:55238400-55242600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:55238400-55244600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:55238400-55249200	Weak transcription	Pancreas	Pancrea
27	chr2:55238400-55249600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:55238400-55250800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr2:55238400-55251200	Weak transcription	Psoas Muscle	Psoas
30	chr2:55238400-55252200	Weak transcription	Fetal Thymus	thymus
31	chr2:55238400-55252400	Weak transcription	Thymus	Thymus
32	chr2:55238400-55253200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:55239200-55243000	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr2:55239200-55244600	Weak transcription	Primary B cells from cord blood	blood
35	chr2:55239200-55244800	Weak transcription	Fetal Muscle Leg	muscle
36	chr2:55239200-55247800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:55239400-55243200	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr2:55239400-55243400	Genic enhancers	HSMM	muscle
39	chr2:55239400-55244800	Enhancers	Muscle Satellite Cultured Cells	--
40	chr2:55239400-55245000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr2:55239600-55243600	Weak transcription	Aorta	Aorta
42	chr2:55239800-55242800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:55239800-55243400	Enhancers	Brain Angular Gyrus	brain
44	chr2:55240000-55244800	Weak transcription	Dnd41	blood
45	chr2:55240200-55244400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:55240400-55244000	Enhancers	NHDF-Ad	bronchial
47	chr2:55240400-55244800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr2:55240400-55249200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:55240400-55249800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr2:55240600-55242600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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