Variant report

Variant	rs56865301
Chromosome Location	chr3:51573062-51573063
allele	C/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	EP300	chr3:51572373-51573134	SK-N-SH	brain:	n/a	chr3:51572966-51572975 chr3:51572745-51572754 chr3:51572780-51572796 chr3:51572908-51572924
2	POLR2A	chr3:51572381-51573215	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:51572279-51574093	IMR90	lung:	n/a	n/a
4	POLR2A	chr3:51572272-51573064	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr3:51572276-51573159	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:51572404-51573088	GM10847	blood:	n/a	n/a
7	POLR2A	chr3:51572365-51573075	K562	blood:	n/a	n/a
8	POLR2A	chr3:51572447-51573155	MCF-7	breast:	n/a	n/a
9	POLR2A	chr3:51572423-51573073	HepG2	liver:	n/a	n/a
10	YY1	chr3:51572411-51573062	H1-hESC	embryonic stem cell:	n/a	chr3:51572779-51572793 chr3:51572966-51572977 chr3:51572963-51572977 chr3:51572744-51572753 chr3:51572960-51572974 chr3:51572782-51572796
11	POLR2A	chr3:51572346-51573259	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:51572412-51573077	ProgFib	skin:	n/a	n/a
13	BHLHE40	chr3:51572085-51573094	GM12878	blood:	n/a	chr3:51572904-51572920
14	YY1	chr3:51572239-51573268	H1-hESC	embryonic stem cell:	n/a	chr3:51572779-51572793 chr3:51572966-51572977 chr3:51572963-51572977 chr3:51572744-51572753 chr3:51572960-51572974 chr3:51572782-51572796
15	MAZ	chr3:51571979-51574231	IMR90	lung:	n/a	n/a
16	CCNT2	chr3:51572506-51573318	K562	blood:	n/a	n/a
17	TAF1	chr3:51572251-51573402	H1-hESC	embryonic stem cell:	n/a	n/a
18	SMARCC1	chr3:51572092-51573853	Hela-S3	cervix:	n/a	chr3:51573789-51573798 chr3:51573631-51573640
19	CHD1	chr3:51572585-51573120	H1-hESC	embryonic stem cell:	n/a	n/a
20	YY1	chr3:51572445-51573160	GM12892	blood:	n/a	chr3:51572779-51572793 chr3:51572966-51572977 chr3:51572963-51572977 chr3:51572744-51572753 chr3:51572960-51572974 chr3:51572782-51572796
21	TAF7	chr3:51572409-51573092	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr3:51572410-51573083	H1-hESC	embryonic stem cell:	n/a	n/a
23	ELF1	chr3:51572414-51573466	GM12878	blood:	n/a	chr3:51572744-51572753 chr3:51572786-51572798 chr3:51573101-51573113
24	POLR2A	chr3:51572441-51573153	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:51572331-51573111	HUVEC	blood vessel:	n/a	n/a
26	GABPA	chr3:51572403-51573165	K562	blood:	n/a	chr3:51572690-51572699
27	HMGN3	chr3:51572345-51573136	K562	blood:	n/a	n/a
28	POLR2A	chr3:51572296-51573086	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr3:51572272-51573063	GM12878	blood:	n/a	n/a
30	MXI1	chr3:51571741-51574162	SK-N-SH	brain:	n/a	n/a
31	TBP	chr3:51572198-51573609	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr3:51572395-51573070	K562	blood:	n/a	n/a
33	YY1	chr3:51572461-51573071	GM12891	blood:	n/a	chr3:51572779-51572793 chr3:51572966-51572977 chr3:51572963-51572977 chr3:51572744-51572753 chr3:51572960-51572974 chr3:51572782-51572796
34	POLR2A	chr3:51572049-51573235	K562	blood:	n/a	n/a
35	TAF7	chr3:51572410-51573094	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr3:51572191-51573688	GM19193	blood:	n/a	n/a
37	POLR2A	chr3:51572126-51573119	PBDE	blood:	n/a	n/a
38	MYC	chr3:51572585-51573347	H1-hESC	embryonic stem cell:	n/a	n/a
39	UBTF	chr3:51572306-51573685	K562	blood:	n/a	n/a
40	CREB1	chr3:51572376-51573153	HepG2	liver:	n/a	n/a
41	YY1	chr3:51572531-51573094	K562	blood:	n/a	chr3:51572779-51572793 chr3:51572966-51572977 chr3:51572963-51572977 chr3:51572744-51572753 chr3:51572960-51572974 chr3:51572782-51572796
42	POLR2A	chr3:51572099-51573090	GM15510	blood:	n/a	n/a
43	POLR2A	chr3:51572285-51573156	GM12892	blood:	n/a	n/a
44	POLR2A	chr3:51572359-51573093	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr3:51572007-51573747	GM18505	blood:	n/a	n/a
46	POLR2A	chr3:51572182-51573135	HUVEC	blood vessel:	n/a	n/a
47	CHD1	chr3:51571910-51574678	IMR90	lung:	n/a	n/a
48	POLR2A	chr3:51572091-51573144	GM12892	blood:	n/a	n/a
49	POLR2A	chr3:51572207-51573098	HEK293	kidney:	n/a	n/a
50	SMARCB1	chr3:51572410-51573744	Hela-S3	cervix:	n/a	chr3:51573631-51573640

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:51573058-51573108	SK-N-SH	brain:	n/a
2	chr3:51573058-51573108	K562	blood:	n/a
3	chr3:51573058-51573108	HEEpiC	esophagus:	n/a
4	chr3:51573036-51573086	NT2-D1	testis:	n/a
5	chr3:51573058-51573108	HepG2	liver:	n/a
6	chr3:51573036-51573086	GM12892	blood:	n/a
7	chr3:51573036-51573086	Hela-S3	cervix:	n/a
8	chr3:51573036-51573086	HCM	heart:	n/a
9	chr3:51573036-51573086	HCT-116	colon:	n/a
10	chr3:51573036-51573086	HRCEpiC	kidney:	n/a
11	chr3:51573058-51573108	HPAEpiC	pulmonary alveolar:	n/a
12	chr3:51573058-51573108	GM06990	blood:	n/a
13	chr3:51573036-51573086	LNCaP	prostate:	n/a
14	chr3:51573058-51573108	BJ	skin:	n/a
15	chr3:51573058-51573108	SK-N-MC	brain:	n/a
16	chr3:51573036-51573086	T-47D	breast:	n/a
17	chr3:51573058-51573108	IMR90	lung:	fetal
18	chr3:51573058-51573108	HL-60	blood:	n/a
19	chr3:51573058-51573108	MCF10A-Er-Src	breast:	n/a
20	chr3:51573058-51573108	RPTEC	kidney:	n/a
21	chr3:51573036-51573086	H1-hESC	embryonic stem cell:	embryo
22	chr3:51573036-51573086	CMK	blood:	n/a
23	chr3:51573058-51573108	AG04449	skin:	fetal
24	chr3:51573058-51573108	HNPCEpiC	eye:	n/a
25	chr3:51573058-51573108	HRE	kidney:	n/a
26	chr3:51573058-51573108	T-47D	breast:	n/a
27	chr3:51573058-51573108	AG10803	skin:	n/a
28	chr3:51573036-51573086	PANC-1	pancreas:	n/a
29	chr3:51573036-51573086	AG04449	skin:	fetal
30	chr3:51573058-51573108	GM19239	blood:	n/a
31	chr3:51573058-51573108	HCT-116	colon:	n/a
32	chr3:51573036-51573086	Hepatocyte	liver:	n/a
33	chr3:51573036-51573086	GM19239	blood:	n/a
34	chr3:51573058-51573108	NHDF-neo	bronchial:	n/a
35	chr3:51573036-51573086	Jurkat	blood:	n/a
36	chr3:51573036-51573086	K562	blood:	n/a
37	chr3:51573036-51573086	ProgFib	skin:	n/a
38	chr3:51573036-51573086	ECC-1	luminal epithelium:	n/a
39	chr3:51573036-51573086	AG10803	skin:	n/a
40	chr3:51573058-51573108	HCPEpiC	choroid plexus:	n/a
41	chr3:51573036-51573086	PFSK-1	brain:	n/a
42	chr3:51573036-51573086	NHBE	bronchial:	n/a
43	chr3:51573036-51573086	HEK293	kidney:	embryo
44	chr3:51573036-51573086	HEEpiC	esophagus:	n/a
45	chr3:51573058-51573108	GM12892	blood:	n/a
46	chr3:51573058-51573108	Hela-S3	cervix:	n/a
47	chr3:51573036-51573086	HRE	kidney:	n/a
48	chr3:51573036-51573086	SK-N-SH	brain:	n/a
49	chr3:51573036-51573086	HAEpiC	amniotic membrane:	n/a
50	chr3:51573036-51573086	AG04450	lung:	fetal

No.	Distal block	Cell Line	Cell type
1	chr3:51533211..51536812-chr3:51571944..51573713,3	MCF-7	breast:
2	chr3:51428771..51431051-chr3:51571775..51574665,3	K562	blood:
3	chr3:51537197..51540003-chr3:51571776..51574071,2	MCF-7	breast:
4	chr3:51572655..51573352-chr6:26198749..26199627,2	Hela-S3	cervix:
5	chr3:51571369..51573938-chr3:51651321..51654419,3	MCF-7	breast:
6	chr3:51532461..51534963-chr3:51570709..51574166,3	K562	blood:
7	chr3:51534724..51536284-chr3:51571592..51573333,2	MCF-7	breast:
8	chr3:51569925..51574030-chr3:51574727..51581311,8	MCF-7	breast:
9	chr3:51571143..51574733-chr3:51574758..51577446,3	K562	blood:
10	chr3:51532744..51536241-chr3:51571123..51575595,5	K562	blood:
11	chr3:51424893..51427102-chr3:51572077..51573890,2	MCF-7	breast:
12	chr11:61729765..61730624-chr3:51572571..51573170,2	Hela-S3	cervix:

Variant related genes	Relation type
RAD54L2	TF binding region
RAD54L2	CpG island
ENSG00000197409	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000145041	Chromatin interaction
ENSG00000164080	Chromatin interaction
ENSG00000145050	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs58638756	0.90[AFR][1000 genomes]
rs6768707	0.80[AFR][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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 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	chr3:51571600-51573600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:51571600-51573800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr3:51571600-51574200	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr3:51571600-51574200	Active TSS	HSMM	muscle
5	chr3:51571600-51574200	Active TSS	NHLF	lung
6	chr3:51571800-51573400	Active TSS	Brain Germinal Matrix	brain
7	chr3:51571800-51573600	Active TSS	H1 Cell Line	embryonic stem cell
8	chr3:51572000-51573200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:51572000-51573400	Active TSS	Brain Hippocampus Middle	brain
10	chr3:51572000-51573400	Active TSS	Esophagus	oesophagus
11	chr3:51572000-51573400	Active TSS	Right Ventricle	heart
12	chr3:51572000-51573600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:51572000-51573600	Active TSS	H9 Cell Line	embryonic stem cell
14	chr3:51572000-51573600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:51572000-51573600	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr3:51572000-51573600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:51572000-51573600	Active TSS	Brain Angular Gyrus	brain
18	chr3:51572000-51573600	Active TSS	Fetal Kidney	kidney
19	chr3:51572000-51573600	Active TSS	Placenta Amnion	Placenta Amnion
20	chr3:51572000-51573600	Active TSS	Sigmoid Colon	Sigmoid Colon
21	chr3:51572000-51573600	Active TSS	Stomach Mucosa	stomach
22	chr3:51572000-51573600	Active TSS	K562	blood
23	chr3:51572000-51573800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:51572000-51573800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:51572000-51573800	Active TSS	Aorta	Aorta
26	chr3:51572000-51573800	Active TSS	Fetal Intestine Large	intestine
27	chr3:51572000-51573800	Active TSS	Fetal Intestine Small	intestine
28	chr3:51572000-51573800	Active TSS	Ovary	ovary
29	chr3:51572000-51574000	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr3:51572000-51574000	Active TSS	Psoas Muscle	Psoas
31	chr3:51572000-51574000	Active TSS	Thymus	Thymus
32	chr3:51572000-51574200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:51572000-51574200	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr3:51572000-51574200	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr3:51572000-51574200	Active TSS	A549	lung
36	chr3:51572000-51574400	Active TSS	NHDF-Ad	bronchial
37	chr3:51572200-51573400	Active TSS	Duodenum Mucosa	Duodenum
38	chr3:51572200-51573400	Active TSS	Fetal Heart	heart
39	chr3:51572200-51573400	Active TSS	Fetal Muscle Trunk	muscle
40	chr3:51572200-51573400	Active TSS	Gastric	stomach
41	chr3:51572200-51573400	Active TSS	Left Ventricle	heart
42	chr3:51572200-51573400	Active TSS	Small Intestine	intestine
43	chr3:51572200-51573400	Active TSS	Stomach Smooth Muscle	stomach
44	chr3:51572200-51573400	Active TSS	Spleen	Spleen
45	chr3:51572200-51573600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:51572200-51573600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:51572200-51573600	Active TSS	Brain Anterior Caudate	brain
48	chr3:51572200-51573600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:51572200-51573600	Active TSS	Brain Substantia Nigra	brain
50	chr3:51572200-51573600	Active TSS	Colon Smooth Muscle	Colon

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