Variant report

Variant	esv3462764
Chromosome Location	chr3:158287372-158288474
allele	n/a
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	BRCA1	chr3:158288446-158288534	H1-hESC	embryonic stem cell:	n/a	n/a
2	GTF2F1	chr3:158288341-158288500	H1-hESC	embryonic stem cell:	n/a	n/a
3	KAP1	chr3:158288462-158289266	HEK293	kidney:	n/a	n/a
4	MAX	chr3:158288371-158289635	A549	lung:	n/a	n/a
5	MAX	chr3:158288455-158289656	HCT-116	colon:	n/a	n/a
6	MAX	chr3:158288371-158289667	A549	lung:	n/a	n/a
7	MXI1	chr3:158288266-158289563	IMR90	lung:	n/a	chr3:158288859-158288874 chr3:158288857-158288872
8	MXI1	chr3:158288318-158289697	SK-N-SH	brain:	n/a	chr3:158288859-158288874 chr3:158288857-158288872
9	NR2F2	chr3:158288450-158289482	K562	blood:	n/a	n/a
10	POLR2A	chr3:158288443-158289396	IMR90	lung:	n/a	n/a
11	POLR2A	chr3:158287403-158287581	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr3:158288346-158289371	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:158288307-158289452	MCF10A-Er-Src	breast:	n/a	n/a
14	REST	chr3:158288369-158289548	H1-neurons	neurons:	n/a	n/a
15	RFX5	chr3:158288241-158289510	SK-N-SH	brain:	n/a	chr3:158288858-158288873 chr3:158288855-158288870 chr3:158288859-158288868 chr3:158288856-158288870 chr3:158288858-158288873 chr3:158288858-158288873
16	TAL1	chr3:158287711-158288079	K562	blood:	n/a	chr3:158287863-158287881
17	TBP	chr3:158288447-158289362	K562	blood:	n/a	n/a
18	ZC3H11A	chr3:158288451-158289222	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158284750..158291147-chr3:158359832..158364955,8	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MLF1-1	chr3:158288342-158288499	l_2517_chr3:158282276-158289024_testes
2	lnc-LXN-1	chr3:158287960-158288012	NONHSAT092927
3	lnc-LXN-1	chr3:158287960-158288855	ENSG00000243150
4	lnc-LXN-1	chr3:158287960-158288130	NONHSAT092926

Variant related genes	Relation type
MLF1	TF binding region
ENSG00000168827	chromatin interactions
RAB8B	miRNA target sites

Extended variants
information (count: 41 )
Associated
traits (count: 49 )

Variant overlapped rSNPs/rCNVs (count:41 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs547190295	chr3:158287374-158287375	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs549277882	chr3:158287396-158287397	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs567045037	chr3:158287413-158287414	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs144089626	chr3:158287448-158287449	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs2276773	chr3:158287455-158287456	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
6	rs148632929	chr3:158287470-158287471	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs9814215	chr3:158287533-158287534	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs554039493	chr3:158287541-158287542	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs572207737	chr3:158287568-158287569	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs536459684	chr3:158287590-158287591	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs554774378	chr3:158287615-158287616	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs141184147	chr3:158287665-158287666	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs544749079	chr3:158287667-158287668	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs58034569	chr3:158287689-158287690	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs572846144	chr3:158287699-158287700	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs578006234	chr3:158287704-158287705	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs150750217	chr3:158287731-158287732	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs569956250	chr3:158287745-158287746	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs139043430	chr3:158287762-158287763	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs16829116	chr3:158287801-158287802	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
21	rs542893044	chr3:158287836-158287837	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs143992840	chr3:158287869-158287870	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs146632887	chr3:158287883-158287884	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs564204426	chr3:158287884-158287885	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs17696609	chr3:158287887-158287888	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs1714515	chr3:158287918-158287919	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
27	rs140204842	chr3:158287980-158287981	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
28	rs532979794	chr3:158287986-158287987	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
29	rs186426615	chr3:158287988-158287989	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
30	rs536180170	chr3:158288018-158288019	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
31	rs545035167	chr3:158288095-158288096	Enhancers Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
32	rs369042973	chr3:158288096-158288097	Enhancers Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
33	rs59973861	chr3:158288103-158288104	Enhancers Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
34	rs190877644	chr3:158288115-158288116	Enhancers Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
35	rs76327551	chr3:158288190-158288191	Enhancers Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
36	rs143776262	chr3:158288216-158288217	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
37	rs556695864	chr3:158288221-158288222	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
38	rs578003625	chr3:158288266-158288267	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
39	rs553976338	chr3:158288282-158288283	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
40	rs553907295	chr3:158288445-158288446	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
41	rs572389849	chr3:158288454-158288455	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:49)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	21115979	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Hepatocellular carcinoma	16750200	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Basal cell lymphoma	17170743	CNVD
Breast cancer	16608533	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	20729466	CNVD
Non-small cell lung cancer	19010865	CNVD
abnormal development	18461090	CNVD
Prostate cancer	18632612	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Colorectal cancer	16272173	CNVD
Prostate cancer	16547154	CNVD
Breast cancer	21364760	CNVD
Gastrointestinal stromal cancer	20818650	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158284400-158288000	Weak transcription	Brain Angular Gyrus	brain
2	chr3:158284400-158288400	Weak transcription	NHEK	skin
3	chr3:158284600-158288400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:158284600-158288400	Weak transcription	Psoas Muscle	Psoas
5	chr3:158285000-158288400	Enhancers	Fetal Heart	heart
6	chr3:158286400-158287600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:158286600-158288400	Weak transcription	HUVEC	blood vessel
8	chr3:158286800-158287800	Enhancers	Right Ventricle	heart
9	chr3:158287000-158288200	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr3:158287200-158288200	Weak transcription	A549	lung
11	chr3:158287600-158287800	Enhancers	Fetal Muscle Trunk	muscle
12	chr3:158287600-158287800	Enhancers	Left Ventricle	heart
13	chr3:158287600-158288400	Enhancers	Fetal Muscle Leg	muscle
14	chr3:158287600-158288400	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr3:158287600-158288400	Enhancers	K562	blood
16	chr3:158287800-158288200	Enhancers	Brain Hippocampus Middle	brain
17	chr3:158287800-158288200	Enhancers	Ovary	ovary
18	chr3:158287800-158288400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:158287800-158288400	Enhancers	Fetal Lung	lung
20	chr3:158287800-158288400	Weak transcription	Right Ventricle	heart
21	chr3:158287800-158288600	Weak transcription	Left Ventricle	heart
22	chr3:158288000-158288200	Enhancers	Brain Anterior Caudate	brain
23	chr3:158288000-158288200	Enhancers	Colon Smooth Muscle	Colon
24	chr3:158288000-158288200	Enhancers	Stomach Smooth Muscle	stomach
25	chr3:158288000-158288400	Enhancers	Brain Angular Gyrus	brain
26	chr3:158288000-158288400	Enhancers	Brain Cingulate Gyrus	brain
27	chr3:158288200-158288400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:158288200-158288400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:158288200-158288400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:158288200-158288400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:158288200-158288400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:158288200-158288400	Enhancers	Muscle Satellite Cultured Cells	--
33	chr3:158288200-158288400	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr3:158288200-158288400	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr3:158288200-158288400	Enhancers	Fetal Brain Female	brain
36	chr3:158288200-158288400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:158288200-158288400	Enhancers	Fetal Stomach	stomach
38	chr3:158288200-158288400	Enhancers	Rectal Smooth Muscle	rectum
39	chr3:158288200-158288400	Enhancers	A549	lung
40	chr3:158288200-158288400	Enhancers	NH-A	brain
41	chr3:158288200-158288400	Enhancers	NHLF	lung
42	chr3:158288200-158288600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
43	chr3:158288200-158288600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
44	chr3:158288200-158288600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:158288200-158288600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
46	chr3:158288200-158288600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:158288200-158288600	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr3:158288200-158288600	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr3:158288200-158288600	Enhancers	HMEC	breast
50	chr3:158288200-158288800	Flanking Active TSS	Brain Anterior Caudate	brain

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