Variant report

Variant	rs2564941
Chromosome Location	chr3:53080148-53080149
allele	A/C
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	PML	chr3:53079598-53081008	GM12878	blood:	n/a	n/a
2	E2F4	chr3:53079633-53080347	K562	blood:	n/a	chr3:53080114-53080123 chr3:53080104-53080113 chr3:53080016-53080027
3	POLR2A	chr3:53079619-53081065	Raji	blood:	n/a	n/a
4	ELF1	chr3:53079606-53081209	GM12878	blood:	n/a	chr3:53080399-53080412
5	MAZ	chr3:53078861-53081185	GM12878	blood:	n/a	n/a
6	MAX	chr3:53079606-53080905	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr3:53079683-53080713	A549	lung:	n/a	n/a
8	POLR2A	chr3:53079923-53080312	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr3:53079654-53080245	HCT-116	colon:	n/a	n/a
10	TAF1	chr3:53079893-53080348	K562	blood:	n/a	n/a
11	EGR1	chr3:53079783-53080274	ECC-1	luminal epithelium:	n/a	chr3:53080115-53080128 chr3:53080114-53080124 chr3:53080110-53080119 chr3:53080104-53080113 chr3:53080118-53080128 chr3:53080120-53080134
12	NRF1	chr3:53079911-53080278	H1-hESC	embryonic stem cell:	n/a	chr3:53080102-53080113 chr3:53080114-53080123 chr3:53080103-53080112 chr3:53080103-53080114 chr3:53080100-53080114 chr3:53080105-53080114 chr3:53080103-53080117
13	POLR2A	chr3:53079700-53081059	PBDE	blood:	n/a	n/a
14	TAF1	chr3:53079751-53080298	ECC-1	luminal epithelium:	n/a	n/a
15	BCLAF1	chr3:53079955-53080354	GM12878	blood:	n/a	n/a
16	MAX	chr3:53079637-53080982	HCT-116	colon:	n/a	n/a
17	MAX	chr3:53078739-53080587	HepG2	liver:	n/a	n/a
18	TAF1	chr3:53079590-53080694	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr3:53079822-53080320	K562	blood:	n/a	n/a
20	MAX	chr3:53079590-53080765	K562	blood:	n/a	n/a
21	POLR2A	chr3:53078724-53081152	GM12892	blood:	n/a	n/a
22	YY1	chr3:53079834-53080318	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr3:53079632-53081014	GM12878	blood:	n/a	n/a
24	ZNF143	chr3:53079813-53081141	GM12878	blood:	n/a	n/a
25	NRF1	chr3:53079931-53080260	Hela-S3	cervix:	n/a	chr3:53080102-53080113 chr3:53080114-53080123 chr3:53080103-53080112 chr3:53080103-53080114 chr3:53080100-53080114 chr3:53080105-53080114 chr3:53080103-53080117
26	YY1	chr3:53079806-53080327	GM12878	blood:	n/a	n/a
27	CREB1	chr3:53079608-53080444	HepG2	liver:	n/a	n/a
28	POLR2A	chr3:53079628-53080590	ECC-1	luminal epithelium:	n/a	n/a
29	MAX	chr3:53080071-53081023	A549	lung:	n/a	n/a
30	ZBTB7A	chr3:53079944-53080450	K562	blood:	n/a	n/a
31	SMC3	chr3:53080120-53080148	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr3:53078745-53081057	GM19099	blood:	n/a	n/a
33	NANOG	chr3:53079921-53080315	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr3:53080027-53080197	Spleen_OC	spleen:	n/a	n/a
35	HMGN3	chr3:53078698-53080815	K562	blood:	n/a	n/a
36	POLR2A	chr3:53079854-53080313	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr3:53079051-53080741	A549	lung:	n/a	n/a
38	REST	chr3:53079573-53080778	H1-neurons	neurons:	n/a	chr3:53080121-53080134
39	POLR2A	chr3:53079098-53080262	K562	blood:	n/a	n/a
40	YY1	chr3:53079850-53080224	SK-N-SH_RA	brain:	n/a	n/a
41	POLR2A	chr3:53079163-53080857	H1-neurons	neurons:	n/a	n/a
42	REST	chr3:53079628-53080197	HL-60	blood:	n/a	chr3:53080121-53080134
43	CREB1	chr3:53079985-53080258	A549	lung:	n/a	n/a
44	POLR2A	chr3:53078993-53080976	GM19193	blood:	n/a	n/a
45	TAF1	chr3:53079644-53080234	H1-hESC	embryonic stem cell:	n/a	n/a
46	E2F6	chr3:53078744-53080891	K562	blood:	n/a	chr3:53080114-53080123 chr3:53078962-53078977 chr3:53080104-53080113
47	POLR2A	chr3:53079352-53080672	H1-neurons	neurons:	n/a	n/a
48	POLR2A	chr3:53079836-53081083	GM12878	blood:	n/a	n/a
49	MXI1	chr3:53080133-53080204	Hela-S3	cervix:	n/a	n/a
50	HA-E2F1	chr3:53079166-53080752	Hela-S3	cervix:	n/a	chr3:53080114-53080123 chr3:53080104-53080113

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:33999620..34000214-chr3:53080089..53080662,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRKCD-2	chr3:53080091-53082182	NONHSAT089977

Variant related genes	Relation type
SFMBT1	TF binding region
ENSG00000101019	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11707780	0.80[EUR][1000 genomes]
rs11712653	0.80[EUR][1000 genomes]
rs11713171	0.80[EUR][1000 genomes]
rs11718388	0.80[EUR][1000 genomes]
rs13072818	0.80[EUR][1000 genomes]
rs1346719	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17052727	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34121720	0.80[EUR][1000 genomes]
rs34340609	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3806692	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3821872	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58660500	0.80[EUR][1000 genomes]
rs6445555	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6445556	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6445557	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71301808	0.80[EUR][1000 genomes]
rs750474	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9756317	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv876800	chr3:53038786-53113762	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1823728	chr3:53046712-53080351	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv1820544	chr3:53046712-53096394	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv822094	chr3:53059674-53096460	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3341503	chr3:53078462-53080760	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv3461090	chr3:53078737-53081285	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv20159	chr3:53078811-53080407	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv1807284	chr3:53078838-53080351	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv1840185	chr3:53078838-53080351	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv590343	chr3:53078892-53080351	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	esv3461089	chr3:53078962-53080610	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	esv3461091	chr3:53078962-53080610	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv590346	chr3:53079048-53080351	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv590347	chr3:53079048-53088815	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv590349	chr3:53079101-53080254	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	esv1798557	chr3:53079101-53080351	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	esv1803812	chr3:53079101-53080351	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	esv1804993	chr3:53079101-53080351	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	esv1824004	chr3:53079101-53080351	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	esv1828710	chr3:53079101-53080351	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	esv1839794	chr3:53079101-53080351	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	esv1841778	chr3:53079101-53080351	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	esv1842789	chr3:53079101-53080351	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
25	esv1849809	chr3:53079101-53080351	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
26	esv1851359	chr3:53079101-53080351	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
27	nsv590350	chr3:53079101-53080351	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
28	nsv590351	chr3:53079152-53080254	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
29	esv1807290	chr3:53079152-53080351	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
30	nsv590352	chr3:53079152-53080351	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
31	nsv590353	chr3:53079268-53080254	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
32	nsv590354	chr3:53079268-53080351	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
33	nsv590355	chr3:53079327-53080351	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53077800-53080800	Active TSS	Right Atrium	heart
2	chr3:53078000-53081200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:53078200-53080200	Active TSS	Colonic Mucosa	Colon
4	chr3:53078200-53080800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr3:53078200-53080800	Active TSS	Small Intestine	intestine
6	chr3:53078200-53081200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr3:53078400-53080200	Active TSS	Right Ventricle	heart
8	chr3:53078400-53080600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr3:53078400-53080600	Active TSS	Placenta	Placenta
10	chr3:53078400-53080600	Active TSS	Pancreas	Pancrea
11	chr3:53078400-53080800	Active TSS	Esophagus	oesophagus
12	chr3:53078400-53081200	Active TSS	H9 Cell Line	embryonic stem cell
13	chr3:53078400-53081200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:53078400-53081200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:53078600-53080200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:53078600-53080200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:53078600-53080400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:53078600-53080400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr3:53078600-53080400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:53078600-53080400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr3:53078600-53080400	Active TSS	Gastric	stomach
22	chr3:53078600-53080400	Active TSS	Left Ventricle	heart
23	chr3:53078600-53080400	Active TSS	GM12878-XiMat	blood
24	chr3:53078600-53080600	Active TSS	Brain Hippocampus Middle	brain
25	chr3:53078600-53080600	Active TSS	Placenta Amnion	Placenta Amnion
26	chr3:53078600-53080600	Active TSS	Psoas Muscle	Psoas
27	chr3:53078600-53080800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr3:53078600-53080800	Active TSS	Brain Cingulate Gyrus	brain
29	chr3:53078600-53080800	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr3:53078600-53080800	Active TSS	Fetal Intestine Small	intestine
31	chr3:53078600-53080800	Active TSS	Sigmoid Colon	Sigmoid Colon
32	chr3:53078600-53080800	Active TSS	HSMMtube	muscle
33	chr3:53078600-53081000	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr3:53078600-53081000	Active TSS	Aorta	Aorta
35	chr3:53078600-53081000	Active TSS	Colon Smooth Muscle	Colon
36	chr3:53078600-53081000	Active TSS	Ovary	ovary
37	chr3:53078600-53081200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
38	chr3:53078600-53081200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:53078600-53081200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:53078600-53081200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:53078600-53081200	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr3:53078600-53081200	Active TSS	HSMM	muscle
43	chr3:53078600-53081400	Active TSS	Fetal Intestine Large	intestine
44	chr3:53078600-53081400	Active TSS	A549	lung
45	chr3:53078600-53081800	Active TSS	Rectal Smooth Muscle	rectum
46	chr3:53078800-53080200	Active TSS	Spleen	Spleen
47	chr3:53078800-53080400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:53078800-53080400	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr3:53078800-53080400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:53078800-53080400	Active TSS	Skeletal Muscle Female	skeletal muscle

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