Variant report

Variant	rs553907295
Chromosome Location	chr3:158288445-158288446
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	MAX	chr3:158288371-158289667	A549	lung:	n/a	n/a
2	MXI1	chr3:158288266-158289563	IMR90	lung:	n/a	chr3:158288859-158288874 chr3:158288857-158288872
3	POLR2A	chr3:158288307-158289452	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr3:158288443-158289396	IMR90	lung:	n/a	n/a
5	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
6	POLR2A	chr3:158288346-158289371	H1-hESC	embryonic stem cell:	n/a	n/a
7	GTF2F1	chr3:158288341-158288500	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr3:158288371-158289635	A549	lung:	n/a	n/a
9	REST	chr3:158288369-158289548	H1-neurons	neurons:	n/a	n/a
10	MXI1	chr3:158288318-158289697	SK-N-SH	brain:	n/a	chr3:158288859-158288874 chr3:158288857-158288872

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-LXN-1	chr3:158287960-158288855	ENSG00000243150
2	lnc-MLF1-1	chr3:158288342-158288499	l_2517_chr3:158282276-158289024_testes

Variant related genes	Relation type
MLF1	TF binding region
ENSG00000168827	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1014381	chr3:158070451-158350118	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv877690	chr3:158184263-158296916	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv916167	chr3:158240540-158320581	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv877691	chr3:158245883-158359667	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1013242	chr3:158275578-158305894	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1013112	chr3:158280085-158301728	Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1001944	chr3:158280085-158305210	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv999408	chr3:158280085-158316431	Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv3462764	chr3:158287372-158288474	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158287800-158288600	Weak transcription	Left Ventricle	heart
2	chr3:158288200-158288600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr3:158288200-158288600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
4	chr3:158288200-158288600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:158288200-158288600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
6	chr3:158288200-158288600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:158288200-158288600	Flanking Active TSS	Brain Hippocampus Middle	brain
8	chr3:158288200-158288600	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr3:158288200-158288600	Enhancers	HMEC	breast
10	chr3:158288200-158288800	Flanking Active TSS	Brain Anterior Caudate	brain
11	chr3:158288200-158288800	Flanking Active TSS	Colon Smooth Muscle	Colon
12	chr3:158288200-158288800	Flanking Active TSS	NHDF-Ad	bronchial
13	chr3:158288200-158289400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr3:158288200-158289600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:158288200-158290000	Active TSS	Brain Substantia Nigra	brain
16	chr3:158288200-158290200	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr3:158288200-158290600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:158288400-158288600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
19	chr3:158288400-158288600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
20	chr3:158288400-158288600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
21	chr3:158288400-158288600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:158288400-158288600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
23	chr3:158288400-158288600	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
24	chr3:158288400-158288600	Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr3:158288400-158288600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:158288400-158288600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
27	chr3:158288400-158288600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
28	chr3:158288400-158288600	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr3:158288400-158288600	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr3:158288400-158288600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:158288400-158288600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:158288400-158288600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:158288400-158288600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:158288400-158288600	Enhancers	Liver	Liver
35	chr3:158288400-158288600	Flanking Active TSS	Brain Angular Gyrus	brain
36	chr3:158288400-158288600	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr3:158288400-158288600	Flanking Active TSS	Fetal Brain Female	brain
38	chr3:158288400-158288600	Active TSS	Fetal Muscle Trunk	muscle
39	chr3:158288400-158288600	Bivalent/Poised TSS	Stomach Mucosa	stomach
40	chr3:158288400-158288600	Enhancers	HSMM	muscle
41	chr3:158288400-158288600	Enhancers	HUVEC	blood vessel
42	chr3:158288400-158288600	Flanking Active TSS	K562	blood
43	chr3:158288400-158288600	Active TSS	NHEK	skin
44	chr3:158288400-158288600	Flanking Active TSS	NHLF	lung
45	chr3:158288400-158288800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:158288400-158288800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:158288400-158288800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
48	chr3:158288400-158288800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:158288400-158288800	Bivalent/Poised TSS	Primary B cells from cord blood	blood
50	chr3:158288400-158288800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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