Variant report

Variant	rs56337137
Chromosome Location	chr2:64247170-64247171
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	chr2:64245682-64247362	A549	lung:	n/a	chr2:64246699-64246706 chr2:64246699-64246709 chr2:64246699-64246708
2	MAX	chr2:64245807-64247301	A549	lung:	n/a	chr2:64246699-64246706 chr2:64246699-64246709 chr2:64246699-64246708
3	FOXA2	chr2:64246613-64247175	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:64246188-64247291	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr2:64246329-64247229	GM12891	blood:	n/a	n/a
6	HEY1	chr2:64245343-64247327	HepG2	liver:	n/a	chr2:64247192-64247201 chr2:64246048-64246063
7	POLR2A	chr2:64246218-64247210	HCT-116	colon:	n/a	n/a
8	NR2F2	chr2:64246509-64247320	K562	blood:	n/a	chr2:64247008-64247023 chr2:64247012-64247027
9	REST	chr2:64245367-64247177	H1-neurons	neurons:	n/a	chr2:64246077-64246090
10	POLR2A	chr2:64246185-64247192	HepG2	liver:	n/a	n/a
11	POLR2A	chr2:64246208-64247232	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr2:64245470-64247182	IMR90	lung:	n/a	n/a
13	NR2F2	chr2:64246572-64247399	HepG2	liver:	n/a	chr2:64247008-64247023 chr2:64247012-64247027
14	MYC	chr2:64245334-64247267	K562	blood:	n/a	chr2:64246699-64246706 chr2:64246699-64246709 chr2:64246699-64246708
15	ATF2	chr2:64246751-64247350	GM12878	blood:	n/a	n/a
16	POLR2A	chr2:64246577-64247254	U87	brain:	n/a	n/a
17	NR2F2	chr2:64246344-64247391	K562	blood:	n/a	chr2:64247008-64247023 chr2:64247012-64247027
18	ARID3A	chr2:64247140-64247364	K562	blood:	n/a	n/a
19	SMC3	chr2:64246256-64247182	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr2:64246950-64247253	HCT-116	colon:	n/a	n/a
21	MXI1	chr2:64246067-64247235	IMR90	lung:	n/a	n/a
22	NR2C2	chr2:64246739-64247196	GM12878	blood:	n/a	chr2:64247008-64247023 chr2:64247010-64247023
23	ARID3A	chr2:64246717-64247240	HepG2	liver:	n/a	n/a
24	IRF1	chr2:64246380-64247345	K562	blood:	n/a	n/a
25	MBD4	chr2:64246488-64247461	HepG2	liver:	n/a	n/a
26	POLR2A	chr2:64245442-64247221	HepG2	liver:	n/a	n/a
27	MTA3	chr2:64246503-64247377	GM12878	blood:	n/a	n/a
28	POLR2A	chr2:64246184-64247306	HepG2	liver:	n/a	n/a
29	MYC	chr2:64246274-64247194	K562	blood:	n/a	chr2:64246699-64246706 chr2:64246699-64246709 chr2:64246699-64246708
30	NFIC	chr2:64246649-64247963	HepG2	liver:	n/a	n/a
31	MBD4	chr2:64246590-64247237	HepG2	liver:	n/a	n/a
32	NR2C2	chr2:64246405-64247229	HepG2	liver:	n/a	chr2:64247008-64247023 chr2:64247010-64247023
33	RCOR1	chr2:64246884-64247281	K562	blood:	n/a	n/a
34	HNF4G	chr2:64246709-64247269	HepG2	liver:	n/a	chr2:64247012-64247024 chr2:64247010-64247023 chr2:64247010-64247023 chr2:64247010-64247024 chr2:64247011-64247023 chr2:64247010-64247025 chr2:64247008-64247026 chr2:64247011-64247024 chr2:64247011-64247023 chr2:64247011-64247023 chr2:64247010-64247023 chr2:64247011-64247023 chr2:64247010-64247024
35	FOXA1	chr2:64246187-64247208	HepG2	liver:	n/a	n/a
36	POLR2A	chr2:64244932-64247847	MCF10A-Er-Src	breast:	n/a	n/a
37	EP300	chr2:64246234-64247236	HepG2	liver:	n/a	n/a
38	MYBL2	chr2:64246449-64247300	HepG2	liver:	n/a	n/a
39	POLR2A	chr2:64246165-64247289	U87	brain:	n/a	n/a
40	MXI1	chr2:64244747-64247333	SK-N-SH	brain:	n/a	n/a
41	TEAD4	chr2:64246543-64247400	HepG2	liver:	n/a	n/a
42	HNF4G	chr2:64246412-64247220	HepG2	liver:	n/a	chr2:64247012-64247024 chr2:64247010-64247023 chr2:64247010-64247023 chr2:64247010-64247024 chr2:64247011-64247023 chr2:64247010-64247025 chr2:64247008-64247026 chr2:64247011-64247024 chr2:64247011-64247023 chr2:64247011-64247023 chr2:64247010-64247023 chr2:64247011-64247023 chr2:64247010-64247024
43	SP1	chr2:64246529-64247311	A549	lung:	n/a	chr2:64246685-64246694 chr2:64246954-64246968 chr2:64246775-64246789 chr2:64246954-64246964 chr2:64246685-64246694 chr2:64246684-64246693 chr2:64246955-64246964
44	MAX	chr2:64245341-64247265	HepG2	liver:	n/a	chr2:64246699-64246706 chr2:64246699-64246709 chr2:64246699-64246708
45	CUX1	chr2:64246743-64247326	K562	blood:	n/a	chr2:64247166-64247180
46	ZNF263	chr2:64245322-64247439	HEK293-T-REx	kidney:	n/a	chr2:64245972-64245981 chr2:64247061-64247082
47	MTA3	chr2:64246817-64247293	GM12878	blood:	n/a	n/a
48	NR2F2	chr2:64246094-64247359	MCF-7	breast:	n/a	chr2:64247008-64247023 chr2:64247012-64247027
49	CHD2	chr2:64246487-64247237	GM12878	blood:	n/a	n/a
50	NFIC	chr2:64246441-64247391	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:64247077..64249106-chr20:57556171..57557833,2	MCF-7	breast:
2	chr2:64246663..64249169-chr2:64259470..64260972,2	K562	blood:
3	chr2:64246318..64247877-chr2:64269595..64271484,2	MCF-7	breast:
4	chr2:64246955..64249358-chr2:64255526..64257239,3	K562	blood:
5	chr2:64226896..64229641-chr2:64246459..64249027,4	K562	blood:

Variant related genes	Relation type
VPS54	TF binding region
ENSG00000101158	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs55666948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55728742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56227836	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59985181	0.85[EUR][1000 genomes]
rs60012302	0.82[EUR][1000 genomes]
rs62621453	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv2763643	chr2:64219887-64281337	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64244600-64247200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:64244600-64247400	Active TSS	Brain Angular Gyrus	brain
3	chr2:64244800-64247200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:64244800-64247200	Active TSS	Psoas Muscle	Psoas
5	chr2:64244800-64247200	Active TSS	Right Atrium	heart
6	chr2:64245000-64247200	Active TSS	H9 Cell Line	embryonic stem cell
7	chr2:64245000-64247200	Active TSS	Fetal Muscle Trunk	muscle
8	chr2:64245200-64247200	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr2:64245400-64247400	Active TSS	Brain Anterior Caudate	brain
10	chr2:64246600-64247200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:64246600-64247200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
12	chr2:64246600-64247200	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr2:64246600-64247200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr2:64246600-64247200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:64246600-64247200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
16	chr2:64246600-64247200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr2:64246600-64247200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:64246600-64247200	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr2:64246600-64247200	Active TSS	Fetal Brain Male	brain
20	chr2:64246600-64247200	Flanking Active TSS	Thymus	Thymus
21	chr2:64246600-64247200	Flanking Active TSS	Dnd41	blood
22	chr2:64246600-64247200	Flanking Active TSS	HUVEC	blood vessel
23	chr2:64246600-64247400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr2:64246600-64247400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:64246600-64247400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr2:64246600-64247800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:64246800-64247200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
28	chr2:64246800-64247200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:64246800-64247200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:64246800-64247200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:64246800-64247200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr2:64246800-64247200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr2:64246800-64247200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr2:64246800-64247200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr2:64246800-64247200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:64246800-64247200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr2:64246800-64247200	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr2:64246800-64247200	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr2:64246800-64247200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:64246800-64247200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr2:64246800-64247200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr2:64246800-64247200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:64246800-64247200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr2:64246800-64247200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:64246800-64247200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:64246800-64247200	Flanking Active TSS	Liver	Liver
47	chr2:64246800-64247200	Flanking Active TSS	Brain Germinal Matrix	brain
48	chr2:64246800-64247200	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr2:64246800-64247200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:64246800-64247200	Flanking Active TSS	Colonic Mucosa	Colon

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