Variant report

Variant	rs73937514
Chromosome Location	chr2:54892527-54892528
allele	G/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	POLR2A	chr2:54892417-54892798	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:54892478-54893065	GM12892	blood:	n/a	n/a
3	POLR2A	chr2:54892468-54893011	GM12891	blood:	n/a	n/a
4	CTCF	chr2:54892489-54892925	H1-hESC	embryonic stem cell:	n/a	chr2:54892717-54892738 chr2:54892715-54892733 chr2:54892716-54892732
5	RAD21	chr2:54892481-54893033	A549	lung:	n/a	chr2:54892716-54892735 chr2:54892775-54892784
6	POLR2A	chr2:54892181-54896917	GM12878	blood:	n/a	n/a
7	RAD21	chr2:54892419-54893102	HCT-116	colon:	n/a	chr2:54892716-54892735 chr2:54892775-54892784
8	SMC3	chr2:54892410-54892906	HepG2	liver:	n/a	chr2:54892717-54892731
9	POLR2A	chr2:54892163-54894444	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:54892397-54893100	HepG2	liver:	n/a	n/a
11	SMC3	chr2:54892514-54892894	K562	blood:	n/a	chr2:54892717-54892731
12	TEAD4	chr2:54892355-54893147	HepG2	liver:	n/a	n/a
13	CTCF	chr2:54892504-54892901	A549	lung:	n/a	chr2:54892717-54892738 chr2:54892715-54892733 chr2:54892716-54892732
14	RAD21	chr2:54892479-54893003	ECC-1	luminal epithelium:	n/a	chr2:54892716-54892735 chr2:54892775-54892784
15	RAD21	chr2:54892505-54892916	H1-hESC	embryonic stem cell:	n/a	chr2:54892716-54892735 chr2:54892775-54892784
16	POLR2A	chr2:54892478-54893074	GM12892	blood:	n/a	n/a
17	POLR2A	chr2:54889935-54893954	K562	blood:	n/a	n/a
18	POLR2A	chr2:54889669-54901118	HepG2	liver:	n/a	n/a
19	RAD21	chr2:54892415-54893054	HepG2	liver:	n/a	chr2:54892716-54892735 chr2:54892775-54892784
20	POLR2A	chr2:54892335-54892959	HepG2	liver:	n/a	n/a
21	CTCF	chr2:54892469-54893001	HepG2	liver:	n/a	chr2:54892717-54892738 chr2:54892715-54892733 chr2:54892716-54892732
22	ZNF263	chr2:54892471-54892863	HEK293-T-REx	kidney:	n/a	chr2:54892655-54892676
23	CTCF	chr2:54892440-54892590	WI-38	lung:	n/a	n/a
24	RAD21	chr2:54892498-54893015	H1-hESC	embryonic stem cell:	n/a	chr2:54892716-54892735 chr2:54892775-54892784
25	POLR2A	chr2:54892412-54893077	GM12891	blood:	n/a	n/a
26	CTCF	chr2:54892423-54892900	K562	blood:	n/a	chr2:54892717-54892738 chr2:54892715-54892733 chr2:54892716-54892732
27	CTCF	chr2:54892418-54893025	HCT-116	colon:	n/a	chr2:54892717-54892738 chr2:54892715-54892733 chr2:54892716-54892732
28	POLR2A	chr2:54892202-54893025	HepG2	liver:	n/a	n/a
29	CTCF	chr2:54892460-54892610	A549	lung:	n/a	n/a
30	POLR2A	chr2:54892517-54892846	H1-neurons	neurons:	n/a	n/a
31	RAD21	chr2:54892505-54892975	H1-hESC	embryonic stem cell:	n/a	chr2:54892716-54892735 chr2:54892775-54892784
32	CTCF	chr2:54892218-54893698	A549	lung:	n/a	chr2:54892717-54892738 chr2:54892715-54892733 chr2:54892716-54892732
33	POLR2A	chr2:54892497-54893268	Hela-S3	cervix:	n/a	n/a
34	CTCF	chr2:54892504-54892935	GM12878	blood:	n/a	chr2:54892717-54892738 chr2:54892715-54892733 chr2:54892716-54892732
35	POLR2A	chr2:54892455-54892715	GM12892	blood:	n/a	n/a
36	EP300	chr2:54892504-54893032	HepG2	liver:	n/a	n/a
37	CTCF	chr2:54892511-54892938	K562	blood:	n/a	chr2:54892717-54892738 chr2:54892715-54892733 chr2:54892716-54892732
38	POLR2A	chr2:54892273-54895690	A549	lung:	n/a	n/a
39	BACH1	chr2:54892480-54892808	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr2:54892522-54892923	GM12892	blood:	n/a	n/a
41	CTCF	chr2:54892446-54892930	MCF-7	breast:	n/a	chr2:54892717-54892738 chr2:54892715-54892733 chr2:54892716-54892732
42	CTCF	chr2:54892505-54892904	H1-hESC	embryonic stem cell:	n/a	chr2:54892717-54892738 chr2:54892715-54892733 chr2:54892716-54892732
43	SMC3	chr2:54892526-54892937	GM12878	blood:	n/a	chr2:54892717-54892731
44	POLR2A	chr2:54892162-54893784	GM12878	blood:	n/a	n/a
45	MBD4	chr2:54892477-54893452	HepG2	liver:	n/a	n/a
46	USF2	chr2:54892511-54892871	Hela-S3	cervix:	n/a	n/a
47	RAD21	chr2:54892471-54892955	MCF-7	breast:	n/a	chr2:54892716-54892735 chr2:54892775-54892784
48	CTCF	chr2:54892380-54892530	GM12871	blood:	n/a	n/a
49	RAD21	chr2:54892429-54892936	HCT-116	colon:	n/a	chr2:54892716-54892735 chr2:54892775-54892784
50	RAD21	chr2:54892527-54892890	SK-N-SH_RA	brain:	n/a	chr2:54892716-54892735 chr2:54892775-54892784

No.	Distal block	Cell Line	Cell type
1	chr2:54786715..54789713-chr2:54890702..54893003,2	K562	blood:
2	chr2:54891251..54894116-chr2:54898637..54900968,3	MCF-7	breast:
3	chr2:54891342..54894033-chr2:54900112..54903106,2	K562	blood:

Variant related genes	Relation type
ENSG00000238018	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1431973	1.00[AMR][1000 genomes]
rs1431974	1.00[AMR][1000 genomes]
rs55633042	1.00[AMR][1000 genomes]
rs56196255	1.00[AMR][1000 genomes]
rs56951671	1.00[AMR][1000 genomes]
rs57406175	1.00[AMR][1000 genomes]
rs57539931	1.00[AMR][1000 genomes]
rs57926982	1.00[AMR][1000 genomes]
rs58204287	1.00[AMR][1000 genomes]
rs58924163	1.00[AMR][1000 genomes]
rs58987524	1.00[AMR][1000 genomes]
rs59061110	1.00[AMR][1000 genomes]
rs59402608	1.00[AMR][1000 genomes]
rs60293507	1.00[AMR][1000 genomes]
rs60542617	1.00[AMR][1000 genomes]
rs60611759	1.00[AMR][1000 genomes]
rs6740921	1.00[AMR][1000 genomes]
rs73934512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73934514	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73934808	1.00[AMR][1000 genomes]
rs73934809	1.00[AMR][1000 genomes]
rs73938306	1.00[AMR][1000 genomes]
rs7570695	1.00[AMR][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	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 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	chr2:54838800-54893400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:54839400-54895000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:54841200-54897800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:54846400-54895600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:54846400-54896600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:54846600-54898000	Strong transcription	Dnd41	blood
7	chr2:54846800-54895400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:54861800-54898600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:54862200-54896600	Strong transcription	Primary hematopoietic stem cells	blood
10	chr2:54862400-54892800	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:54862600-54893400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:54862600-54898400	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr2:54863000-54895000	Strong transcription	Duodenum Mucosa	Duodenum
14	chr2:54863000-54898600	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr2:54863000-54899400	Strong transcription	Primary T cells from cord blood	blood
16	chr2:54863600-54897000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
17	chr2:54863800-54897400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:54863800-54898600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:54864200-54893600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr2:54865400-54892800	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:54865400-54898400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:54865800-54898200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:54866000-54892800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr2:54866400-54897200	Strong transcription	Primary B cells from cord blood	blood
25	chr2:54867200-54892800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:54867200-54892800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:54867200-54897800	Strong transcription	Primary B cells from peripheral blood	blood
28	chr2:54867200-54898200	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr2:54868800-54898600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:54869000-54896400	Strong transcription	Colonic Mucosa	Colon
31	chr2:54869600-54893400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:54869600-54898600	Strong transcription	Fetal Thymus	thymus
33	chr2:54869800-54895200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:54869800-54897600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:54870000-54892600	Strong transcription	Right Ventricle	heart
36	chr2:54870000-54892600	Strong transcription	HMEC	breast
37	chr2:54870200-54893000	Strong transcription	Fetal Brain Female	brain
38	chr2:54870600-54892800	Strong transcription	Brain Germinal Matrix	brain
39	chr2:54878400-54897000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:54879200-54893000	Weak transcription	Psoas Muscle	Psoas
41	chr2:54879600-54898400	Strong transcription	GM12878-XiMat	blood
42	chr2:54880200-54892600	Strong transcription	Fetal Intestine Small	intestine
43	chr2:54880200-54898400	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr2:54880200-54898400	Strong transcription	Thymus	Thymus
45	chr2:54882400-54894800	Weak transcription	K562	blood
46	chr2:54883000-54895000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr2:54883000-54899400	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr2:54885000-54896400	Strong transcription	Hela-S3	cervix
49	chr2:54886200-54892600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:54886200-54893000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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