Variant report

Variant	rs1454423
Chromosome Location	chr2:55647729-55647730
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	MYC	chr2:55646122-55647864	K562	blood:	n/a	chr2:55647250-55647259
2	BHLHE40	chr2:55646315-55648449	GM12878	blood:	n/a	chr2:55647260-55647276
3	STAT3	chr2:55647333-55647861	Hela-S3	cervix:	n/a	n/a
4	BCL3	chr2:55646230-55647945	A549	lung:	n/a	chr2:55647787-55647796 chr2:55647092-55647101 chr2:55647231-55647244
5	MYC	chr2:55645887-55647919	NB4	blood:	n/a	chr2:55647250-55647259
6	JUN	chr2:55645058-55648415	K562	blood:	n/a	chr2:55647729-55647736 chr2:55647728-55647739 chr2:55645468-55645477 chr2:55647729-55647737 chr2:55647729-55647737
7	JUND	chr2:55646854-55647804	H1-hESC	embryonic stem cell:	n/a	chr2:55647729-55647736 chr2:55647728-55647739 chr2:55647729-55647737 chr2:55647729-55647737
8	E2F4	chr2:55646867-55647765	MCF10A-Er-Src	breast:	n/a	chr2:55647254-55647268 chr2:55647193-55647202 chr2:55647251-55647265 chr2:55647235-55647244 chr2:55647231-55647240
9	SIN3A	chr2:55646119-55647828	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr2:55645746-55647971	HepG2	liver:	n/a	chr2:55647250-55647259
11	WRNIP1	chr2:55646950-55647830	GM12878	blood:	n/a	n/a
12	PML	chr2:55645861-55647868	GM12878	blood:	n/a	n/a
13	MXI1	chr2:55646414-55647831	HepG2	liver:	n/a	n/a
14	FOS	chr2:55647544-55647876	MCF10A-Er-Src	breast:	n/a	chr2:55647729-55647736 chr2:55647727-55647738 chr2:55647728-55647739 chr2:55647729-55647737 chr2:55647729-55647737
15	IRF1	chr2:55646746-55647739	K562	blood:	n/a	chr2:55647729-55647738 chr2:55647322-55647336 chr2:55647116-55647130 chr2:55647521-55647541
16	MAFF	chr2:55647575-55647862	K562	blood:	n/a	n/a
17	TBL1XR1	chr2:55646748-55647801	K562	blood:	n/a	n/a
18	SP1	chr2:55646501-55647924	A549	lung:	n/a	chr2:55647118-55647130 chr2:55647119-55647133 chr2:55647323-55647332 chr2:55647120-55647129 chr2:55647019-55647030 chr2:55647020-55647030 chr2:55647322-55647334 chr2:55647119-55647128 chr2:55647119-55647128
19	BHLHE40	chr2:55646736-55647874	K562	blood:	n/a	chr2:55647260-55647276
20	TEAD4	chr2:55646695-55647886	K562	blood:	n/a	n/a
21	POLR2A	chr2:55646158-55647745	H1-hESC	embryonic stem cell:	n/a	n/a
22	MXI1	chr2:55646294-55647810	H1-hESC	embryonic stem cell:	n/a	n/a
23	NFIC	chr2:55646174-55647827	HepG2	liver:	n/a	n/a
24	YY1	chr2:55646218-55647738	H1-hESC	embryonic stem cell:	n/a	chr2:55647231-55647240 chr2:55647231-55647245 chr2:55647232-55647246 chr2:55647213-55647222
25	CEBPB	chr2:55646894-55647842	Hela-S3	cervix:	n/a	n/a
26	TCF12	chr2:55645747-55647747	A549	lung:	n/a	n/a
27	RCOR1	chr2:55645573-55647980	IMR90	lung:	n/a	n/a
28	ZNF263	chr2:55645848-55647777	HEK293-T-REx	kidney:	n/a	n/a
29	MBD4	chr2:55646463-55647797	HepG2	liver:	n/a	n/a
30	MYC	chr2:55646948-55647934	MCF10A-Er-Src	breast:	n/a	chr2:55647250-55647259
31	PBX3	chr2:55646241-55647938	A549	lung:	n/a	n/a
32	FOS	chr2:55646982-55647883	HUVEC	blood vessel:	n/a	chr2:55647729-55647736 chr2:55647727-55647738 chr2:55647728-55647739 chr2:55647729-55647737 chr2:55647729-55647737
33	MYC	chr2:55646065-55648003	A549	lung:	n/a	chr2:55647250-55647259
34	MAX	chr2:55646246-55647907	SK-N-SH	brain:	n/a	chr2:55647250-55647259
35	MAX	chr2:55646213-55647856	K562	blood:	n/a	chr2:55647250-55647259
36	RCOR1	chr2:55646829-55647814	K562	blood:	n/a	n/a
37	SMARCC1	chr2:55645820-55647746	Hela-S3	cervix:	n/a	n/a
38	MAX	chr2:55645785-55647879	NB4	blood:	n/a	chr2:55647250-55647259
39	MXI1	chr2:55646979-55647881	K562	blood:	n/a	n/a
40	MXI1	chr2:55644654-55648547	SK-N-SH	brain:	n/a	n/a
41	MAZ	chr2:55645809-55647820	K562	blood:	n/a	chr2:55647250-55647259
42	MYC	chr2:55645930-55647878	K562	blood:	n/a	chr2:55647250-55647259
43	MAX	chr2:55645689-55648008	A549	lung:	n/a	chr2:55647250-55647259
44	KAP1	chr2:55646897-55647783	HEK293	kidney:	n/a	n/a
45	TAF1	chr2:55646321-55647768	PFSK-1	brain:	n/a	n/a
46	JUND	chr2:55645637-55647867	K562	blood:	n/a	chr2:55647728-55647739 chr2:55647729-55647737 chr2:55647729-55647736 chr2:55647729-55647737
47	MAX	chr2:55646053-55647859	ECC-1	luminal epithelium:	n/a	chr2:55647250-55647259
48	BHLHE40	chr2:55646750-55647774	HepG2	liver:	n/a	chr2:55647260-55647276
49	BRCA1	chr2:55647449-55647931	Hela-S3	cervix:	n/a	n/a
50	ATF3	chr2:55646763-55647755	A549	lung:	n/a	chr2:55647255-55647264 chr2:55647237-55647246

No.	Distal block	Cell Line	Cell type
1	chr2:55643936..55648492-chr2:55843198..55848689,6	K562	blood:
2	chr2:55458950..55461087-chr2:55647562..55649544,2	K562	blood:
3	chr2:55644452..55648722-chr2:55843350..55848689,7	K562	blood:
4	chr2:55645285..55648583-chr2:55745099..55748276,4	K562	blood:
5	chr2:55647253..55647758-chr2:55659096..55659834,2	K562	blood:
6	chr2:55508669..55511212-chr2:55645960..55648569,3	MCF-7	breast:
7	chr2:55645285..55648583-chr2:55744780..55749543,7	K562	blood:
8	chr2:55646864..55647857-chr2:70417660..70418658,2	Hela-S3	cervix:
9	chr2:55508571..55512777-chr2:55645734..55648780,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC104-5	chr2:55646412-55648361	NONHSAT070787

Variant related genes	Relation type
CCDC88A	TF binding region
ENSG00000272606	Chromatin interaction
ENSG00000162997	Chromatin interaction
ENSG00000163001	Chromatin interaction
ENSG00000138041	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000115998	Chromatin interaction
ENSG00000143947	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10182704	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10184756	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10195081	0.81[AFR][1000 genomes]
rs10454144	0.88[EUR][1000 genomes]
rs11125565	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11125566	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11125572	0.93[ASN][1000 genomes]
rs11695152	0.83[AFR][1000 genomes]
rs12612806	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12617891	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12618216	0.92[ASN][1000 genomes]
rs12618795	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12623954	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713297	0.86[ASN][1000 genomes]
rs13416912	0.84[EUR][1000 genomes]
rs1454415	0.98[ASN][1000 genomes]
rs1454419	1.00[ASN][1000 genomes]
rs1454420	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1454424	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545554	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1902056	0.93[EUR][1000 genomes]
rs1902057	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1902058	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1902061	0.90[ASN][1000 genomes]
rs1902062	0.82[ASN][1000 genomes]
rs2045132	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2045133	0.93[EUR][1000 genomes]
rs2045134	0.96[ASN][1000 genomes]
rs2045135	0.98[ASN][1000 genomes]
rs2045136	0.91[ASN][1000 genomes]
rs2123983	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2219130	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2576688	0.90[EUR][1000 genomes]
rs2576703	0.90[EUR][1000 genomes]
rs2589057	0.90[EUR][1000 genomes]
rs2589068	0.90[EUR][1000 genomes]
rs2589069	0.90[EUR][1000 genomes]
rs2589070	0.90[EUR][1000 genomes]
rs2589078	0.90[EUR][1000 genomes]
rs2589079	0.90[EUR][1000 genomes]
rs2589104	0.90[EUR][1000 genomes]
rs2864831	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2864832	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2867173	0.90[EUR][1000 genomes]
rs2867178	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2867179	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2867194	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2902857	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2903507	0.93[EUR][1000 genomes]
rs2903509	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2903514	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2917777	0.90[EUR][1000 genomes]
rs2920970	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2966466	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3099080	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3099081	0.90[EUR][1000 genomes]
rs3099083	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3111408	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3111409	0.95[EUR][1000 genomes]
rs3748943	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762511	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3974263	0.90[EUR][1000 genomes]
rs4233960	0.90[EUR][1000 genomes]
rs4233961	0.93[EUR][1000 genomes]
rs4277563	0.98[ASN][1000 genomes]
rs4481025	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4535081	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672032	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672033	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672036	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4672037	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4672038	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4672040	0.98[ASN][1000 genomes]
rs4672041	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672043	0.93[ASN][1000 genomes]
rs4672044	0.93[ASN][1000 genomes]
rs59634508	0.90[EUR][1000 genomes]
rs61157332	0.90[EUR][1000 genomes]
rs6545489	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545490	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6545491	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6545492	0.98[ASN][1000 genomes]
rs6709204	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6710192	0.93[EUR][1000 genomes]
rs6718031	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6718909	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6720698	0.97[ASN][1000 genomes]
rs6721593	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6724840	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6725968	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6729490	0.81[AFR][1000 genomes]
rs6732633	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6732759	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6733814	0.98[ASN][1000 genomes]
rs6744426	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6748979	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72924907	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7424286	0.94[ASN][1000 genomes]
rs7557555	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7557956	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7579037	0.98[ASN][1000 genomes]
rs7586440	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7601588	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7602189	0.98[ASN][1000 genomes]
rs7606361	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][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	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55642600-55648200	Active TSS	GM12878-XiMat	blood
2	chr2:55643000-55648000	Active TSS	Brain Germinal Matrix	brain
3	chr2:55643200-55648000	Active TSS	Fetal Brain Female	brain
4	chr2:55643200-55648200	Active TSS	Brain Cingulate Gyrus	brain
5	chr2:55643200-55648200	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr2:55643800-55648000	Active TSS	NHDF-Ad	bronchial
7	chr2:55643800-55648400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:55643800-55648400	Active TSS	NHLF	lung
9	chr2:55644000-55648000	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr2:55644000-55648000	Active TSS	Brain Angular Gyrus	brain
11	chr2:55644000-55648000	Active TSS	Brain Substantia Nigra	brain
12	chr2:55644000-55648400	Active TSS	Brain Anterior Caudate	brain
13	chr2:55644200-55647800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:55644200-55647800	Active TSS	Brain Hippocampus Middle	brain
15	chr2:55644200-55648000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:55644200-55648200	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr2:55644200-55648400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:55644400-55647800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:55644400-55647800	Active TSS	Duodenum Mucosa	Duodenum
20	chr2:55644400-55647800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr2:55644400-55648000	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr2:55644400-55648000	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr2:55644400-55648000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:55644400-55648000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:55644400-55648000	Active TSS	Fetal Kidney	kidney
26	chr2:55644400-55648000	Active TSS	HSMMtube	muscle
27	chr2:55644400-55648200	Active TSS	Muscle Satellite Cultured Cells	--
28	chr2:55644600-55647800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:55644600-55647800	Active TSS	HSMM	muscle
30	chr2:55644600-55647800	Active TSS	NH-A	brain
31	chr2:55644600-55648000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:55644600-55648000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:55644600-55648000	Active TSS	Fetal Stomach	stomach
34	chr2:55644600-55648200	Active TSS	A549	lung
35	chr2:55644800-55647800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:55644800-55648000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:55644800-55648000	Active TSS	Osteobl	bone
38	chr2:55645000-55647800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:55645000-55648000	Active TSS	Colon Smooth Muscle	Colon
40	chr2:55645200-55647800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr2:55645200-55648000	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr2:55645200-55648000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:55645400-55647800	Active TSS	Fetal Lung	lung
44	chr2:55645400-55648000	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr2:55645600-55647800	Active TSS	H9 Cell Line	embryonic stem cell
46	chr2:55645600-55647800	Active TSS	Right Ventricle	heart
47	chr2:55645600-55648000	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr2:55645600-55648000	Active TSS	Aorta	Aorta
49	chr2:55645600-55648000	Active TSS	Fetal Muscle Trunk	muscle
50	chr2:55645600-55648000	Active TSS	Ovary	ovary

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